JASPAR

Names
More detailed information about this field from each metasource.

JASPAR
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

jaspar
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

Other names: jaspar

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.

Webpage:

http://jaspar.genereg.net

Licence:

Name: CC-BY-4.0

Publications: (8)

Publications
More detailed information about this field from each metasource.

JASPAR: an open-access database for eukaryotic transcription factor binding profiles
PMID: 14681366
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
PMID: 24194598
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
PMID: 26531826
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
PMID: 18006571
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
PMID: 19906716
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

A new generation of JASPAR, the open-access repository for transcription factor binding site profiles
PMID: 16381983
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

JASPAR RESTful API: accessing JASPAR data from any programming language
PMID: 29253085
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

http://dx.doi.org/10.1093/nar/gkx1126
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:53.352250

JASPAR: an open-access database for eukaryotic transcription factor binding profiles PubMed citations: 759.

759 articles citing: JASPAR: an open-access database for eukaryotic transcription factor binding profiles

Serine 727 phosphorylation is necessary to induce the STAT3-mediated transcription of LINC00184 in oesophageal squamous cell carcinoma. PMID:35312906
The arginine methyltransferase PRMT7 promotes extravasation of monocytes resulting in tissue injury in COPD. PMID:35288557
Interaction of lncRNA MIR100HG with hnRNPA2B1 facilitates m6A-dependent stabilization of TCF7L2 mRNA and colorectal cancer progression. PMID:35279145
Estrogen Receptor-Beta2 (ERβ2)-Mutant p53-FOXM1 Axis: A Novel Driver of Proliferation, Chemoresistance, and Disease Progression in High Grade Serous Ovarian Cancer (HGSOC). PMID:35267428
EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells. PMID:35182476
Transcriptomic analysis reveals myometrial topologically associated domains linked to the onset of human term labour. PMID:35150271
Identification of Potential Key Genes and Molecular Mechanisms of Medulloblastoma Based on Integrated Bioinformatics Approach. PMID:35127939
JAK2/STAT3 inhibition attenuates intestinal ischemia-reperfusion injury via promoting autophagy: in vitro and in vivo study. PMID:35067814
Astrocyte-Derived Pleiotrophin Mitigates Late-Stage Autoimmune CNS Inflammation. PMID:35046956
Gene regulation network analyses of pistil development in papaya. PMID:34983382
Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. PMID:34965939
Ginsenoside Rg1 Inhibits Microglia Pyroptosis Induced by Lipopolysaccharide Through Regulating STAT3 Signaling. PMID:34908862
Network Analysis of Microarray Data. PMID:34902128
Spatial transcriptomics reveals gene expression characteristics in invasive micropapillary carcinoma of the breast. PMID:34799559
Prenatal interleukin 6 elevation increases glutamatergic synapse density and disrupts hippocampal connectivity in offspring. PMID:34758338
Cancer drivers and clonal dynamics in acute lymphoblastic leukaemia subtypes. PMID:34753926
Fast activation maximization for molecular sequence design. PMID:34670493
Identification and Characterisation of cis-Regulatory Elements Upstream of the Human Receptor Tyrosine Kinase Gene MERTK. PMID:34631417
Expression of cell proliferation regulatory factors bricd5, tnfrsf21, cdk1 correlates with expression of clock gene cry1 in testes of Hu rams during puberty. PMID:34626314
SBSA: an online service for somatic binding sequence annotation. PMID:34606615
VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. PMID:34570217
Systematic Evaluation of DNA Sequence Variations on in vivo Transcription Factor Binding Affinity. PMID:34567058
TooManyPeaks identifies drug-resistant-specific regulatory elements from single-cell leukemic epigenomes. PMID:34433064
Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization. PMID:34417622
Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome. PMID:34417209
Distinct regulation of hippocampal neuroplasticity and ciliary genes by corticosteroid receptors. PMID:34362910
Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes. PMID:34340684
Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis. PMID:34316701
Perturbations of the Proteome and of Secreted Metabolites in Primary Astrocytes from the hSOD1(G93A) ALS Mouse Model. PMID:34209958
Dysregulation of the secretory pathway connects Alzheimer's disease genetics to aggregate formation. PMID:34171228
BACH1 Binding Links the Genetic Risk for Severe Periodontitis with ST8SIA1. PMID:34160287
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data. PMID:34125906
The Chromatin Accessibility Landscape of Peripheral Blood Mononuclear Cells in Patients With Systemic Lupus Erythematosus at Single-Cell Resolution. PMID:34084162
MafF Is an Antiviral Host Factor That Suppresses Transcription from Hepatitis B Virus Core Promoter. PMID:33980595
Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes. PMID:33978759
Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions. PMID:33975875
Scrt1, a transcriptional regulator of β-cell proliferation identified by differential chromatin accessibility during islet maturation. PMID:33888791
Morphological and genomic shifts in mole-rat 'queens' increase fecundity but reduce skeletal integrity. PMID:33843584
Sequence-based GWAS and post-GWAS analyses reveal a key role of SLC37A1, ANKH, and regulatory regions on bovine milk mineral content. PMID:33824377
Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing. PMID:33763080
Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites. PMID:33751115
Severe acute respiratory syndrome coronavirus 2 may exploit human transcription factors involved in retinoic acid and interferon-mediated response: a hypothesis supported by an in silico analysis. PMID:33680474
In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data. PMID:33466789
In silico analysis of promoter regions and regulatory elements (motifs and CpG islands) of the genes encoding for alcohol production in Saccharomyces cerevisiaea S288C and Schizosaccharomyces pombe 972h. PMID:33428031
First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach. PMID:33413117
Whole-genome sequencing reveals insights into the adaptation of French Charolais cattle to Cuban tropical conditions. PMID:33397281
Variable interplay of UV-induced DNA damage and repair at transcription factor binding sites. PMID:33347579
Aortic Gene Expression Profiles Show How ApoA-I Levels Modulate Inflammation, Lysosomal Activity, and Sphingolipid Metabolism in Murine Atherosclerosis. PMID:33327742
The ZNF750-RAC1 axis as potential prognostic factor for breast cancer. PMID:33298895
Gestational arsenic exposure induces site-specific DNA hypomethylation in active retrotransposon subfamilies in offspring sperm in mice. PMID:33267854
Role of Non-Coding Variants in Brugada Syndrome. PMID:33202810
Tnni1b-ECR183-d2, an 87 bp cardiac enhancer of zebrafish. PMID:33194440
Neutralization of S100A4 induces stabilization of atherosclerotic plaques: role of smooth muscle cells. PMID:33135065
SMDB: pivotal somatic sequence alterations reprogramming regulatory cascades. PMID:33094288
DNA mismatches reveal conformational penalties in protein-DNA recognition. PMID:33087930
The reuse of public datasets in the life sciences: potential risks and rewards. PMID:33024631
Comparative Characterization of Two cxcl8 Homologs in Oplegnathus fasciatus: Genomic, Transcriptional and Functional Analyses. PMID:32998424
Highly homologous mouse Cyp2a4 and Cyp2a5 genes are differentially expressed in the liver and both express long non-coding antisense RNAs. PMID:32987105
Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma. PMID:32974985
Conformation of sister chromatids in the replicated human genome. PMID:32968280
In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes-Associated Single Nucleotide Polymorphisms. PMID:32912862
COCOA: coordinate covariation analysis of epigenetic heterogeneity. PMID:32894181
Spatial patterns of CTCF sites define the anatomy of TADs and their boundaries. PMID:32782014
Immune network dysregulation precedes clinical diagnosis of asthma. PMID:32732938
Occupancy maps of 208 chromatin-associated proteins in one human cell type. PMID:32728244
Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis. PMID:32725242
Identification and Functional Annotation of Genes Related to Horses' Performance: From GWAS to Post-GWAS. PMID:32664293
Klf9 is a key feedforward regulator of the transcriptomic response to glucocorticoid receptor activity. PMID:32651405
Targeted sequencing of genes associated with the mismatch repair pathway in patients with endometrial cancer. PMID:32634176
Single-cell ATAC-seq signal extraction and enhancement with SCATE. PMID:32620137
Inhibition of Skp2 Sensitizes Chronic Myeloid Leukemia Cells to Imatinib. PMID:32606967
RNA-seq reveals downregulated osteochondral genes potentially related to tibia bacterial chondronecrosis with osteomyelitis in broilers. PMID:32493207
fcScan: a versatile tool to cluster combinations of sites using genomic coordinates. PMID:32429868
Galectin-3 modulates epithelial cell adaptation to stress at the ER-mitochondria interface. PMID:32398681
TLR9 Sensing of Self-DNA Controls Cell-Mediated Immunity to Listeria Infection via Rapid Conversion of Conventional CD4+ T Cells to Treg. PMID:32268093
Redox-mediated regulation of aging and healthspan by an evolutionarily conserved transcription factor HLH-2/Tcf3/E2A. PMID:32203922
HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer. PMID:32154941
Chloroquine and Rapamycin Augment Interleukin-37 Expression via the LC3, ERK, and AP-1 Axis in the Presence of Lipopolysaccharides. PMID:32104716
Sex differences in spiders: from phenotype to genomics. PMID:32052129
Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells. PMID:32043966
DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD. PMID:32020675
A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. PMID:31995498
Pan-cancer analysis of somatic mutations and epigenetic alterations in insulated neighbourhood boundaries. PMID:31945090
Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46. PMID:31840818
Metabolic Control of Astrocyte Pathogenic Activity via cPLA2-MAVS. PMID:31813625
Functional genomic approaches to elucidate the role of enhancers during development. PMID:31808313
The landscape of tiered regulation of breast cancer cell metabolism. PMID:31780802
Common DNA sequence variation influences 3-dimensional conformation of the human genome. PMID:31779666
Genetic variants of VEGFR-1 gene promoter in acute myocardial infarction. PMID:31744542
FA2H Exhibits Tumor Suppressive Roles on Breast Cancers via Cancer Stemness Control. PMID:31709178
JASPAR 2020: update of the open-access database of transcription factor binding profiles. PMID:31701148
A Bayesian Framework for Inferring the Influence of Sequence Context on Point Mutations. PMID:31651955
The Hsp90 Molecular Chaperone Regulates the Transcription Factor Network Controlling Chromatin Accessibility. PMID:31628945
Regulation of lifespan by neural excitation and REST. PMID:31619788
Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability. PMID:31595288
Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels. PMID:31578528
Gene expression profiling of skeletal myogenesis in human embryonic stem cells reveals a potential cascade of transcription factors regulating stages of myogenesis, including quiescent/activated satellite cell-like gene expression. PMID:31560727
Enhancer activation by FGF signalling during otic induction. PMID:31539539
Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. PMID:31533632
CiiiDER: A tool for predicting and analysing transcription factor binding sites. PMID:31483836
The Putative Association of TOB1-AS1 Long Non-coding RNA with Immune Tolerance: A Study on Multiple Sclerosis Patients. PMID:31482275
Regulation of Cyclin E by transcription factors of the naïve pluripotency network in mouse embryonic stem cells. PMID:31462142
The Cdk2-c-Myc-miR-571 Axis Regulates DNA Replication and Genomic Stability by Targeting Geminin. PMID:31431461
Genome-wide identification and expression profiling of the C2H2-type zinc finger protein genes in the silkworm Bombyx mori. PMID:31316872
Opposing transcriptional and post-transcriptional roles for Scalloped in binary Hippo-dependent neural fate decisions. PMID:31265830
The protein secretion modulator TMED9 drives CNIH4/TGFα/GLI signaling opposing TMED3-WNT-TCF to promote colon cancer metastases. PMID:31253868
lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells. PMID:31182783
Tau accumulation triggers STAT1-dependent memory deficits by suppressing NMDA receptor expression. PMID:31085626
Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. PMID:31061989
DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer. PMID:31053176
Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9. PMID:31051141
Tissue-specific sex differences in human gene expression. PMID:31044242
Allele-specific enhancers mediate associations between LCAT and ABCA1 polymorphisms and HDL metabolism. PMID:31039173
Differential effects on neurodevelopment of FTO variants in obesity and bipolar disorder suggested by in silico prediction of functional impact: An analysis in Mexican population. PMID:31033179
SP1 regulates KLF4 via SP1 binding motif governed by DNA methylation during odontoblastic differentiation of human dental pulp cells. PMID:31009133
DNA-protein interaction: identification, prediction and data analysis. PMID:30915687
Heme Oxygenase 1 Impairs Glucocorticoid Receptor Activity in Prostate Cancer. PMID:30813528
Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases. PMID:30804403
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PMID:30779737
Model-Based Clustering With Data Correction For Removing Artifacts In Gene Expression Data. PMID:30740193
Atypical GATA protein TRPS1 plays indispensable roles in mouse two-cell embryo. PMID:30712485
Mitotic chromosome binding predicts transcription factor properties in interphase. PMID:30700703
EnhancerDB: a resource of transcriptional regulation in the context of enhancers. PMID:30689845
High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue. PMID:30679562
Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages. PMID:30679424
Atypical β-S haplotypes: classification and genetic modulation in patients with sickle cell anemia. PMID:30622282
Human genome-wide measurement of drug-responsive regulatory activity. PMID:30575722
A resource of variant effect predictions of single nucleotide variants in model organisms. PMID:30573687
"Omics" data integration and functional analyses link Enoyl-CoA hydratase, short chain 1 to drug refractory dilated cardiomyopathy. PMID:30541556
A new sequence logo plot to highlight enrichment and depletion. PMID:30526486
Interplay between transcription regulators RUNX1 and FUBP1 activates an enhancer of the oncogene c-KIT and amplifies cell proliferation. PMID:30500954
NRF2-regulated cell cycle arrest at early stage of oxidative stress response mechanism. PMID:30485363
An equivariant Bayesian convolutional network predicts recombination hotspots and accurately resolves binding motifs. PMID:30481258
Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions. PMID:30442124
CNEFinder: finding conserved non-coding elements in genomes. PMID:30423090
Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation. PMID:30379068
MicroRNA expression profile of urinary exosomes in Type IV lupus nephritis complicated by cellular crescent. PMID:30306067
Thirty biologically interpretable clusters of transcription factors distinguish cancer type. PMID:30305013
Dataset on the response of Hut78 cells to novel rexinoids. PMID:30294626
Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis. PMID:30261835
Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation. PMID:30239706
Enhanced vascular activity of a new chimeric promoter containing the full CaMV 35S promoter and the plant XYLOGEN PROTEIN 1 promoter. PMID:30148030
The Prion Protein Regulates Synaptic Transmission by Controlling the Expression of Proteins Key to Synaptic Vesicle Recycling and Exocytosis. PMID:30128651
Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. PMID:30097539
Long noncoding RNA HEGBC promotes tumorigenesis and metastasis of gallbladder cancer via forming a positive feedback loop with IL-11/STAT3 signaling pathway. PMID:30086773
Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis. PMID:30081074
A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks. PMID:29940845
Human-specific features of spatial gene expression and regulation in eight brain regions. PMID:29898898
A comprehensive spatial-temporal transcriptomic analysis of differentiating nascent mouse lens epithelial and fiber cells. PMID:29883638
Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks. PMID:29874603
Synthetic Promoters: Designing the cis Regulatory Modules for Controlled Gene Expression. PMID:29855997
Egr2-independent, Klf1-mediated induction of PD-L1 in CD4+ T cells. PMID:29728568
A novel gene expression analytics-based approach to structure aided design of rexinoids for development as next-generation cancer therapeutics. PMID:29704526
Selection on the regulation of sympathetic nervous activity in humans and chimpanzees. PMID:29672586
Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions. PMID:29659575
A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. PMID:29654311
A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction. PMID:29654070
Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism. PMID:29641996
DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants. PMID:29617928
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. PMID:29617668
Functional and Comparative Genomics of Hoxa2 Gene cis-Regulatory Elements: Evidence for Evolutionary Modification of Ancestral Core Element Activity. PMID:29615583
Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee. PMID:29608722
The DNA methylation profile of liver tumors in C3H mice and identification of differentially methylated regions involved in the regulation of tumorigenic genes. PMID:29566670
A CREB-mediated increase in miRNA let-7f during prolonged β-agonist exposure: a novel mechanism of β2-adrenergic receptor down-regulation in airway smooth muscle. PMID:29455573
Paracrine and epigenetic control of CAF-induced metastasis: the role of HOTAIR stimulated by TGF-ß1 secretion. PMID:29325547
Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes. PMID:29325176
Mediator complex component MED13 regulates zygotic genome activation and is required for postimplantation development in the mouse. PMID:29325037
Sequence motif finder using memetic algorithm. PMID:29298679
RUNX1 regulates site specificity of DNA demethylation by recruitment of DNA demethylation machineries in hematopoietic cells. PMID:29296817
SREBP-2-driven transcriptional activation of human SND1 oncogene. PMID:29296233
THiCweed: fast, sensitive detection of sequence features by clustering big datasets. PMID:29267972
Evidence for a hierarchical transcriptional circuit in Drosophila male germline involving testis-specific TAF and two gene-specific transcription factors, Mod and Acj6. PMID:29235675
MeDReaders: a database for transcription factors that bind to methylated DNA. PMID:29145608
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. PMID:29140473
GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif. PMID:29116820
Denaturing CLIP, dCLIP, Pipeline Identifies Discrete RNA Footprints on Chromatin-Associated Proteins and Reveals that CBX7 Targets 3' UTRs to Regulate mRNA Expression. PMID:29073373
Investigating transcription factor synergism in humans. PMID:29069301
Synthetic RNA-Based Immunomodulatory Gene Circuits for Cancer Immunotherapy. PMID:29056342
The p53-inducible long noncoding RNA TRINGS protects cancer cells from necrosis under glucose starvation. PMID:29046333
HOTAIR but not ANRIL long non-coding RNA contributes to the pathogenesis of multiple sclerosis. PMID:29030863
Logo2PWM: a tool to convert sequence logo to position weight matrix. PMID:28984206
An improved compound Poisson model for the number of motif hits in DNA sequences. PMID:28961747
Identification of breast cancer associated variants that modulate transcription factor binding. PMID:28957321
Rapid Chromatin Switch in the Direct Reprogramming of Fibroblasts to Neurons. PMID:28954238
Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface. PMID:28879060
Combinatorial regulation of a Blimp1 (Prdm1) enhancer in the mouse retina. PMID:28829770
Dual control of pcdh8l/PCNS expression and function in Xenopus laevis neural crest cells by adam13/33 via the transcription factors tfap2α and arid3a. PMID:28829038
Antipsychotic-induced Hdac2 transcription via NF-κB leads to synaptic and cognitive side effects. PMID:28783139
Genetic variability and functional implication of the long control region in HPV-16 variants in Southwest China. PMID:28767682
EMQIT: a machine learning approach for energy based PWM matrix quality improvement. PMID:28764727
Novel atherogenic pathways from the differential transcriptome analysis of diabetic epicardial adipose tissue. PMID:28739185
Investigation of the role of DNA methylation in the expression of ERBB2 in human myocardium. PMID:28735727
Coordinated transcriptional control of adipocyte triglyceride lipase (Atgl) by transcription factors Sp1 and peroxisome proliferator-activated receptor γ (PPARγ) during adipocyte differentiation. PMID:28726642
Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure. PMID:28693562
A Type 2 Diabetes-Associated Functional Regulatory Variant in a Pancreatic Islet Enhancer at the ADCY5 Locus. PMID:28684635
Recurrent and functional regulatory mutations in breast cancer. PMID:28658208
A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells. PMID:28654683
Beyond MITF: Multiple transcription factors directly regulate the cellular phenotype in melanocytes and melanoma. PMID:28649789
A hormonal cue promotes timely follicle cell migration by modulating transcription profiles. PMID:28610887
Gene networks for total number born in pigs across divergent environments. PMID:28577119
Network modelling of gene regulation. PMID:28510232
Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. PMID:28481342
Downregulating ANP32A rescues synapse and memory loss via chromatin remodeling in Alzheimer model. PMID:28472990
Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer. PMID:28423538
SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism. PMID:28369034
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization. PMID:28347313
Stepwise analysis of MIR9 loci identifies miR-9-5p to be involved in Oestrogen regulated pathways in breast cancer patients. PMID:28345661
DNA methylation patterns of behavior-related gene promoter regions dissect the gray wolf from domestic dog breeds. PMID:28321510
Sex-specific, reciprocal regulation of ERα and miR-22 controls muscle lipid metabolism in male mice. PMID:28314781
Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs. PMID:28193157
The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features. PMID:28139710
MEF2C transcription factor is associated with the genetic and epigenetic risk architecture of schizophrenia and improves cognition in mice. PMID:28115742
Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges. PMID:28076869
Inference of hierarchical regulatory network of TCF7L2 binding sites in MCF7 cell line. PMID:28066512
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites. PMID:28035026
Tribbles Pseudokinase 3 Induces Both Apoptosis and Autophagy in Amyloid-β-induced Neuronal Death. PMID:28011637
Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns. PMID:27984582
Non-coding single nucleotide variants affecting estrogen receptor binding and activity. PMID:27964748
OTX2 impedes self-renewal of porcine iPS cells through downregulation of NANOG expression. PMID:27924227
The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6. PMID:27918583
Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation. PMID:27903902
The Inhibition of microRNA-128 on IGF-1-Activating mTOR Signaling Involves in Temozolomide-Induced Glioma Cell Apoptotic Death. PMID:27893811
NRL-Regulated Transcriptome Dynamics of Developing Rod Photoreceptors. PMID:27880916
A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a. PMID:27866707
The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development. PMID:27837089
An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters. PMID:27812284
Evaluating Transcription Factor Activity Changes by Scoring Unexplained Target Genes in Expression Data. PMID:27723775
Parametric bootstrapping for biological sequence motifs. PMID:27716039
Inference of gene regulation functions from dynamic transcriptome data. PMID:27652904
Comparative transcriptome analysis in different tissues of a medicinal herb, Picrorhiza kurroa pinpoints transcription factors regulating picrosides biosynthesis. PMID:27633652
Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. PMID:27526204
Comparative Transcriptional Profiling of Primed and Non-primed Rice Seedlings under Submergence Stress. PMID:27516766
Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. PMID:27468897
Nuclear IKKα mediates microRNA-7/-103/107/21 inductions to downregulate maspin expression in response to HBx overexpression. PMID:27409165
Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome. PMID:27401230
Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington's Disease. PMID:27390852
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Targeting Endothelial Adhesion Molecule Transcription for Treatment of Inflammatory Disease: A Proof-of-Concept Study. PMID:27293321
ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naïve SLE B cells. PMID:27249108
Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events. PMID:27184706
BACH2 regulates CD8(+) T cell differentiation by controlling access of AP-1 factors to enhancers. PMID:27158840
A Maternal System Initiating the Zygotic Developmental Program through Combinatorial Repression in the Ascidian Embryo. PMID:27152625
Identifying Network Perturbation in Cancer. PMID:27145341
Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures. PMID:27143130
Bisphenol A causes reproductive toxicity, decreases dnmt1 transcription, and reduces global DNA methylation in breeding zebrafish (Danio rerio). PMID:27120497
Dysregulation of miRNA-9 in a Subset of Schizophrenia Patient-Derived Neural Progenitor Cells. PMID:27117414
The obesity-induced transcriptional regulator TRIP-Br2 mediates visceral fat endoplasmic reticulum stress-induced inflammation. PMID:27109496
Associations between the MDM2 promoter P1 polymorphism del1518 (rs3730485) and incidence of cancer of the breast, lung, colon and prostate. PMID:27081698
Cis-regulatory architecture of a brain signaling center predates the origin of chordates. PMID:27064252
The retinoblastoma protein regulates hypoxia-inducible genetic programs, tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. PMID:27015368
Function and evolution of local repeats in the Firre locus. PMID:27009974
Identification of Regulatory Mutations in SERPINC1 Affecting Vitamin D Response Elements Associated with Antithrombin Deficiency. PMID:27003919
A Positive Feed-forward Loop Associating EGR1 and PDGFA Promotes Proliferation and Self-renewal in Glioblastoma Stem Cells. PMID:27002148
Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila. PMID:26975664
ChlamyNET: a Chlamydomonas gene co-expression network reveals global properties of the transcriptome and the early setup of key co-expression patterns in the green lineage. PMID:26968660
Identification of chromatin accessibility domains in human breast cancer stem cells. PMID:26962893
The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? PMID:26939991
Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome. PMID:26931148
Computational Characterization of Osteoporosis Associated SNPs and Genes Identified by Genome-Wide Association Studies. PMID:26930606
Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding? PMID:26901046
A variant at 9p21.3 functionally implicates CDKN2B in paediatric B-cell precursor acute lymphoblastic leukaemia aetiology. PMID:26868379
Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis. PMID:26842464
Revealing new candidate genes for reproductive traits in pigs: combining Bayesian GWAS and functional pathways. PMID:26830357
A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. PMID:26823433
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
Genome-wide Association Study of Platelet Count Identifies Ancestry-Specific Loci in Hispanic/Latino Americans. PMID:26805783
Common variation in atrial fibrillation: navigating the path from genetic association to mechanism. PMID:26733238
Insulator dysfunction and oncogene activation in IDH mutant gliomas. PMID:26700815
SVM2Motif--Reconstructing Overlapping DNA Sequence Motifs by Mimicking an SVM Predictor. PMID:26690911
Competition between DNA methylation and transcription factors determines binding of NRF1. PMID:26675734
Abscisic-acid-dependent basic leucine zipper (bZIP) transcription factors in plant abiotic stress. PMID:26669319
Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis. PMID:26668163
Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol. PMID:26637976
Branched-chain amino acid catabolism is a conserved regulator of physiological ageing. PMID:26620638
Inhibition of Lysyl Oxidases Improves Drug Diffusion and Increases Efficacy of Cytotoxic Treatment in 3D Tumor Models. PMID:26620400
Nuclear Factor κB1/RelA Mediates Inflammation in Human Lung Epithelial Cells at Atmospheric Oxygen Levels. PMID:26588041
DiffLogo: a comparative visualization of sequence motifs. PMID:26577052
Genome-Wide Locations of Potential Epimutations Associated with Environmentally Induced Epigenetic Transgenerational Inheritance of Disease Using a Sequential Machine Learning Prediction Approach. PMID:26571271
Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000. PMID:26566919
Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data. PMID:26552868
Evolution of lineage-specific functions in ancient cis-regulatory modules. PMID:26538567
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. PMID:26531826
Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. PMID:26498677
A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence. PMID:26494712
An integrated functional genomic analysis identifies the antitumorigenic mechanism of action for PPARγ in lung cancer cells. PMID:26484153
Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals. PMID:26482678
MicroRNA-223 is a crucial mediator of PPARγ-regulated alternative macrophage activation. PMID:26436647
TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence. PMID:26413153
Endothelial Msx1 transduces hemodynamic changes into an arteriogenic remodeling response. PMID:26391659
ERG promotes the maintenance of hematopoietic stem cells by restricting their differentiation. PMID:26385962
Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene. PMID:26337422
Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. PMID:26314830
YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers. PMID:26295846
Repression of Esophageal Neoplasia and Inflammatory Signaling by Anti-miR-31 Delivery In Vivo. PMID:26286729
Inflammatory regulation of steroid sulfatase: A novel mechanism to control estrogen homeostasis and inflammation in chronic liver disease. PMID:26220752
A Functional SNP in BNC2 Is Associated with Adolescent Idiopathic Scoliosis. PMID:26211971
BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations. PMID:26202972
Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence. PMID:26196144
p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses. PMID:26183718
Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity. PMID:26169829
Cooperative Transcriptional Activation of Antimicrobial Genes by STAT and NF-κB Pathways by Concerted Recruitment of the Mediator Complex. PMID:26146080
Global Gene Expression Changes in Liver Following Hepatocyte Nuclear Factor 4 alpha deletion in Adult Mice. PMID:26120557
Putative regulation mechanism for the MSTN gene by a CpG island generated by the SINE marker Ins227bp. PMID:26100061
Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation. PMID:26099425
FCGR2A Promoter Methylation and Risks for Intravenous Immunoglobulin Treatment Responses in Kawasaki Disease. PMID:26089602
Influence of functional polymorphisms in TNF-α, IL-8, and IL-10 cytokine genes on mRNA expression levels and risk of gastric cancer. PMID:26088449
Direct ChIP-Seq significance analysis improves target prediction. PMID:26040656
Integrative network-based approach identifies key genetic elements in breast invasive carcinoma. PMID:26040466
Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour. PMID:26009010
Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells. PMID:25992972
A SNP in the HTT promoter alters NF-κB binding and is a bidirectional genetic modifier of Huntington disease. PMID:25938884
A property-based analysis of human transcription factors. PMID:25890365
Association analyses confirm five susceptibility loci for systemic lupus erythematosus in the Han Chinese population. PMID:25890262
Molecular development of chondrichthyan claspers and the evolution of copulatory organs. PMID:25868783
FRESCo: finding regions of excess synonymous constraint in diverse viruses. PMID:25853568
SLFN11 Is a Transcriptional Target of EWS-FLI1 and a Determinant of Drug Response in Ewing Sarcoma. PMID:25779942
Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. PMID:25763110
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples. PMID:25725063
Gene co-expression network analysis provides novel insights into myostatin regulation at three different mouse developmental timepoints. PMID:25695797
Eye selector logic for a coordinated cell cycle exit. PMID:25695251
Integrative analysis of 111 reference human epigenomes. PMID:25693563
Signatures of natural selection at the FTO (fat mass and obesity associated) locus in human populations. PMID:25647475
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach. PMID:25627106
Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila. PMID:25609699
Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets. PMID:25583120
Identification and computational analysis of gene regulatory elements. PMID:25561628
Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. PMID:25559185
Identifying causal regulatory SNPs in ChIP-seq enhancers. PMID:25520196
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. PMID:25505144
The promoter of cell growth- and RNA protection-associated SND1 gene is activated by endoplasmic reticulum stress in human hepatoma cells. PMID:25494629
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
Sexually-dimorphic targeting of functionally-related genes in COPD. PMID:25431000
Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction. PMID:25421055
BRCA1 regulation of epidermal growth factor receptor (EGFR) expression in human breast cancer cells involves microRNA-146a and is critical for its tumor suppressor function. PMID:25417703
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. PMID:25378322
CDK6 as a key regulator of hematopoietic and leukemic stem cell activation. PMID:25342715
Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta. PMID:25326687
Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis. PMID:25319994
miR-193a-3p regulates the multi-drug resistance of bladder cancer by targeting the LOXL4 gene and the oxidative stress pathway. PMID:25311867
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways. PMID:25279814
Large differences in global transcriptional regulatory programs of normal and tumor colon cells. PMID:25253512
The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. PMID:25205108
Network biology in medicine and beyond. PMID:25140061
A systems biology approach identified different regulatory networks targeted by KSHV miR-K12-11 in B cells and endothelial cells. PMID:25106478
Structural Features of the Telomerase RNA Gene in the Naked Mole Rat Heterocephalus glaber. PMID:25093110
Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes. PMID:25085117
Systematic analysis of transcription-level effects of neurodegenerative diseases on human brain metabolism by a newly reconstructed brain-specific metabolic network. PMID:25061554
Transient estrogen receptor binding and p300 redistribution support a squelching mechanism for estradiol-repressed genes. PMID:25051172
Research resource: Aorta- and liver-specific ERα-binding patterns and gene regulation by estrogen. PMID:24992180
TGA Transcription Factors Activate the Salicylic Acid-Suppressible Branch of the Ethylene-Induced Defense Program by Regulating ORA59 Expression. PMID:24989234
Transcriptome dynamics of a desert poplar (Populus pruinosa) in response to continuous salinity stress. PMID:24913126
Molecular architecture of transcription factor hotspots in early adipogenesis. PMID:24857666
Motif-based analysis of large nucleotide data sets using MEME-ChIP. PMID:24853928
Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer. PMID:24786295
Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. PMID:24773781
Identification of candidate susceptibility genes for colorectal cancer through eQTL analysis. PMID:24760461
Lsd1 restricts the number of germline stem cells by regulating multiple targets in escort cells. PMID:24625679
Integrative analysis of many RNA-seq datasets to study alternative splicing. PMID:24583115
Active enhancer positions can be accurately predicted from chromatin marks and collective sequence motif data. PMID:24565409
A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data. PMID:24555784
CCAAT enhancer binding protein and nuclear factor of activated T cells regulate HIV-1 LTR via a novel conserved downstream site in cells of the monocyte-macrophage lineage. PMID:24551078
Inherited variation in the PARP1 gene and survival from melanoma. PMID:24535833
EXTREME: an online EM algorithm for motif discovery. PMID:24532725
Genome-wide analysis of functional and evolutionary features of tele-enhancers. PMID:24496725
Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification. PMID:24496624
Effect of dietary n-3 polyunsaturated fatty acids on transcription factor regulation in the bovine endometrium. PMID:24449365
Immune evasion by oncogenic proteins of acute myeloid leukemia. PMID:24449212
Expression and accumulation of the two-domain odorant-binding protein AaegOBP45 in the ovaries of blood-fed Aedes aegypti. PMID:24367904
Reverse engineering the neuroblastoma regulatory network uncovers MAX as one of the master regulators of tumor progression. PMID:24349289
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. PMID:24335146
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data. PMID:24322294
Transcriptional regulatory network and protein-protein interaction to reveal the mechanism of pancreatic cancer. PMID:24307251
Novel factors in the pathogenesis of psoriasis and potential drug candidates are found with systems biology approach. PMID:24303025
Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data. PMID:24267147
Discovering transcription and splicing networks in myelodysplastic syndromes. PMID:24244432
A feed-forward loop involving Trib3, Akt and FoxO mediates death of NGF-deprived neurons. PMID:24212932
Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information. PMID:24204023
AEBP1 upregulation confers acquired resistance to BRAF (V600E) inhibition in melanoma. PMID:24201813
A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells. PMID:24194746
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. PMID:24194598
REST mediates androgen receptor actions on gene repression and predicts early recurrence of prostate cancer. PMID:24163104
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. PMID:24156763
VEGFA rSNPs, transcriptional factor binding sites and human disease. PMID:24097272
Flanking sequence context-dependent transcription factor binding in early Drosophila development. PMID:24093548
A general approach for discriminative de novo motif discovery from high-throughput data. PMID:24057214
Divergent transcriptional regulatory logic at the intersection of tissue growth and developmental patterning. PMID:24039600
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. PMID:23981286
Identification of transcription factor binding sites from ChIP-seq data at high resolution. PMID:23980024
Loss of phosphatase and tensin homolog (PTEN) induces leptin-mediated leptin gene expression: feed-forward loop operating in the lung. PMID:23963458
Optimized position weight matrices in prediction of novel putative binding sites for transcription factors in the Drosophila melanogaster genome. PMID:23936309
Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq. PMID:23865409
Functional evolution of cis-regulatory modules of STMADS11 superclade MADS-box genes. PMID:23860795
Nuclear factor one X regulates Bobby sox during development of the mouse forebrain. PMID:23852417
Global gene expression analysis in human uterine epithelial cells defines new targets of glucocorticoid and estradiol antagonism. PMID:23843231
Impaired cardiovascular function caused by different stressors elicits a common pathological and transcriptional response in zebrafish embryos. PMID:23837677
FADS2 Genetic Variance in Combination with Fatty Acid Intake Might Alter Composition of the Fatty Acids in Brain. PMID:23826354
kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets. PMID:23771147
Uniform, optimal signal processing of mapped deep-sequencing data. PMID:23770639
Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems. PMID:23762209
Mechanosensitive microRNAs-role in endothelial responses to shear stress and redox state. PMID:23727269
NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data. PMID:23706083
The majority of primate-specific regulatory sequences are derived from transposable elements. PMID:23675311
p53 Integrates host defense and cell fate during bacterial pneumonia. PMID:23630228
Identification of transcriptional regulators in the mouse immune system. PMID:23624555
Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites. PMID:23578135
A Common histone modification code on C4 genes in maize and its conservation in Sorghum and Setaria italica. PMID:23564230
VEGFA SNPs and transcriptional factor binding sites associated with high altitude sickness in Han and Tibetan Chinese at the Qinghai-Tibetan Plateau. PMID:23553563
Hypoxia-inducible factor (HIF)-1α and CCN2 form a regulatory circuit in hypoxic nucleus pulposus cells: CCN2 suppresses HIF-1α level and transcriptional activity. PMID:23530034
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PMID:23516347
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. PMID:23512712
Identification of germ cell-specific genes in mammalian meiotic prophase. PMID:23445120
Salicylic acid suppresses jasmonic acid signaling downstream of SCFCOI1-JAZ by targeting GCC promoter motifs via transcription factor ORA59. PMID:23435661
Screening of potential pseudo att sites of Streptomyces phage ΦC31 integrase in the human genome. PMID:23416928
Correlated evolution of positions within mammalian cis elements. PMID:23408994
Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome. PMID:23355428
Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures. PMID:23326246
Hepatocyte nuclear factor 4 alpha deletion promotes diethylnitrosamine-induced hepatocellular carcinoma in rodents. PMID:23315968
MISCORE: a new scoring function for characterizing DNA regulatory motifs in promoter sequences. PMID:23282090
Neuregulin 1-HER axis as a key mediator of hyperglycemic memory effects in breast cancer. PMID:23213231
Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements. PMID:23201014
NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse. PMID:23196988
The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes. PMID:23190768
C/EBPγ deregulation results in differentiation arrest in acute myeloid leukemia. PMID:23160200
2009 pandemic H1N1 influenza virus elicits similar clinical course but differential host transcriptional response in mouse, macaque, and swine infection models. PMID:23153050
A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression. PMID:23110100
Polymorphism rs11085226 in the gene encoding polypyrimidine tract-binding protein 1 negatively affects glucose-stimulated insulin secretion. PMID:23077502
Functional analysis of transcription factor binding sites in human promoters. PMID:22951020
Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. PMID:22938179
Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites. PMID:22913572
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PMID:22912568
Unbiased proteomic analysis of proteins interacting with the HIV-1 5'LTR sequence: role of the transcription factor Meis. PMID:22904091
Vitamin D responsive elements within the HLA-DRB1 promoter region in Sardinian multiple sclerosis associated alleles. PMID:22848563
Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics. PMID:22839973
A common and functional mineralocorticoid receptor haplotype enhances optimism and protects against depression in females. PMID:22832354
Retracted: Luciferase-transfected colon adenocarcinoma cell line (DLD-1) for use in Orthotopic Xenotransplantation studies. PMID:22809083
Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. PMID:22785314
Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays. PMID:22768123
Developmental Coordination of Gene Expression between Synaptic Partners During GABAergic Circuit Assembly in Cerebellar Cortex. PMID:22754500
AKT3, ANGPTL4, eNOS3, and VEGFA associations with high altitude sickness in Han and Tibetan Chinese at the Qinghai-Tibetan Plateau. PMID:22729570
CTCF and Sp1 interact with the Murine gammaherpesvirus 68 internal repeat elements. PMID:22706977
Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling. PMID:22697243
A computational profiling of changes in gene expression and transcription factors induced by vFLIP K13 in primary effusion lymphoma. PMID:22624040
Inferring direct DNA binding from ChIP-seq. PMID:22610855
Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. PMID:22593555
Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach. PMID:22558535
MDM2 promoter SNP344T>A (rs1196333) status does not affect cancer risk. PMID:22558411
Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis. PMID:22509525
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. PMID:22426492
MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. PMID:22424423
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. PMID:22421546
An epigenetic blockade of cognitive functions in the neurodegenerating brain. PMID:22388814
Lens development depends on a pair of highly conserved Sox21 regulatory elements. PMID:22387845
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. PMID:22369687
An SNP selection strategy identified IL-22 associating with susceptibility to tuberculosis in Chinese. PMID:22355539
ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice. PMID:22307325
Genome-wide repression of NF-κB target genes by transcription factor MIBP1 and its modulation by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase. PMID:22294689
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. PMID:22292669
Post-GWAS functional characterization of susceptibility variants for chronic lymphocytic leukemia. PMID:22235315
Sox2 and Mitf cross-regulatory interactions consolidate progenitor and melanocyte lineages in the cranial neural crest. PMID:22186729
A computational pipeline for comparative ChIP-seq analyses. PMID:22179591
Genomic promoter occupancy of runt-related transcription factor RUNX2 in Osteosarcoma cells identifies genes involved in cell adhesion and motility. PMID:22158627
Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers. PMID:22144875
GWASdb: a database for human genetic variants identified by genome-wide association studies. PMID:22139925
Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. PMID:22130890
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities. PMID:22102575
De novo genesis of enhancers in vertebrates. PMID:22069375
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. PMID:22058225
Large-scale motif discovery using DNA Gray code and equiprobable oligomers. PMID:22057160
A motif-independent metric for DNA sequence specificity. PMID:22017798
Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins. PMID:21991322
Unique DNA methylome profiles in CpG island methylator phenotype colon cancers. PMID:21990380
High-throughput analysis of promoter occupancy reveals new targets for Arx, a gene mutated in mental retardation and interneuronopathies. PMID:21966449
Assessing the effects of symmetry on motif discovery and modeling. PMID:21949783
Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development. PMID:21935353
Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns. PMID:21910886
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. PMID:21846408
Transcription factor beacons for the quantitative detection of DNA binding activity. PMID:21815647
Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene. PMID:21812971
Runx2 controls a feed-forward loop between androgen and prolactin-induced protein (PIP) in stimulating T47D cell proliferation. PMID:21809344
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. PMID:21765417
mRNA levels in control rat liver display strain-specific, hereditary, and AHR-dependent components. PMID:21760882
Novel variant of thyroglobulin promoter triggers thyroid autoimmunity through an epigenetic interferon alpha-modulated mechanism. PMID:21757724
The differential disease regulome. PMID:21736759
An integrated ChIP-seq analysis platform with customizable workflows. PMID:21736739
Towards resolving the transcription factor network controlling myelin gene expression. PMID:21729871
MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters. PMID:21708028
Androgen receptor driven transcription in molecular apocrine breast cancer is mediated by FoxA1. PMID:21701558
Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. PMID:21689477
A linear model for transcription factor binding affinity prediction in protein binding microarrays. PMID:21637853
Identification of novel targets of CSL-dependent Notch signaling in hematopoiesis. PMID:21637838
Kinetic profiling of the c-Myc transcriptome and bioinformatic analysis of repressed gene promoters. PMID:21623162
CENTDIST: discovery of co-associated factors by motif distribution. PMID:21602269
Inferring transcription factor complexes from ChIP-seq data. PMID:21602262
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. PMID:21586587
BINOCh: binding inference from nucleosome occupancy changes. PMID:21551136
DREME: motif discovery in transcription factor ChIP-seq data. PMID:21543442
Using polymorphisms in FKBP5 to define biologically distinct subtypes of posttraumatic stress disorder: evidence from endocrine and gene expression studies. PMID:21536970
Using graph theory to analyze biological networks. PMID:21527005
Uncovering the transcriptional circuitry in skeletal muscle regeneration. PMID:21509518
Extensive DNA-binding specificity divergence of a conserved transcription regulator. PMID:21498688
Finding subtypes of transcription factor motif pairs with distinct regulatory roles. PMID:21486752
Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PMID:21445258
Mapping and analysis of chromatin state dynamics in nine human cell types. PMID:21441907
Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites. PMID:21435340
PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers. PMID:21402921
Identification of anchor genes during kidney development defines ontological relationships, molecular subcompartments and regulatory pathways. PMID:21386911
Expression profile analysis of the inflammatory response regulated by hepatocyte nuclear factor 4α. PMID:21352552
Liver X receptor-retinoid X receptor (LXR-RXR) heterodimer cistrome reveals coordination of LXR and AP1 signaling in keratinocytes. PMID:21349840
Expression of the Distalless-B gene in Ciona is regulated by a pan-ectodermal enhancer module. PMID:21338600
Single-nucleotide polymorphisms in LPA explain most of the ancestry-specific variation in Lp(a) levels in African Americans. PMID:21283670
Bioinformatic detection of E47, E2F1 and SREBP1 transcription factors as potential regulators of genes associated to acquisition of endometrial receptivity. PMID:21272326
Transcriptional repression and DNA looping associated with a novel regulatory element in the final exon of the lymphotoxin-β gene. PMID:21248773
Densely interconnected transcriptional circuits control cell states in human hematopoiesis. PMID:21241896
Systematic characterization of protein-DNA interactions. PMID:21207099
Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor. PMID:21183607
A spatial and temporal map of C. elegans gene expression. PMID:21177967
High-throughput mapping of protein occupancy identifies functional elements without the restriction of a candidate factor approach. PMID:21169336
Predicting DNA-binding specificities of eukaryotic transcription factors. PMID:21152420
JUN-CCAAT/enhancer-binding protein complexes inhibit surfactant-associated protein B promoter activity. PMID:21148742
Polymorphisms in genes coding for GRK2 and GRK5 and response differences in antihypertensive-treated patients. PMID:21127457
Initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes. PMID:21125402
A Bayesian search for transcriptional motifs. PMID:21124986
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. PMID:21106904
Reverse engineering the yeast RNR1 transcriptional control system. PMID:21103376
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments. PMID:21081511
A common connexin-40 gene promoter variant affects connexin-40 expression in human atria and is associated with atrial fibrillation. PMID:21076161
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs. PMID:21059262
Alignment-free sequence comparison (II): theoretical power of comparison statistics. PMID:20973742
Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome. PMID:20927350
Theoretical and empirical quality assessment of transcription factor-binding motifs. PMID:20923783
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
Sequence analysis of chromatin immunoprecipitation data for transcription factors. PMID:20827592
A regulatory toolbox of MiniPromoters to drive selective expression in the brain. PMID:20807748
A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. PMID:20736230
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. PMID:20709693
Nicotinic α5 receptor subunit mRNA expression is associated with distant 5' upstream polymorphisms. PMID:20700147
Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example. PMID:20685816
Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development. PMID:20678241
Chondro/osteoblastic and cardiovascular gene modulation in human artery smooth muscle cells that calcify in the presence of phosphate and calcitriol or paricalcitol. PMID:20665672
Research Resource: The androgen receptor modulates expression of genes with critical roles in muscle development and function. PMID:20610535
Characterization of the apoptotic response of human leukemia cells to organosulfur compounds. PMID:20598143
Dynamic CRM occupancy reflects a temporal map of developmental progression. PMID:20571532
A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PMID:20485488
Highly conserved transcriptional responses to mechanical ventilation of the lung. PMID:20460603
GOAL: a software tool for assessing biological significance of genes groups. PMID:20459620
The dissection of transcriptional modules regulated by various drugs of abuse in the mouse striatum. PMID:20459597
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. PMID:20438625
Identification and characterization of putative methylation targets in the MAOA locus using bioinformatic approaches. PMID:20421737
MochiView: versatile software for genome browsing and DNA motif analysis. PMID:20409324
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. PMID:20409305
Genome-wide comparison between IL-17 and combined TNF-alpha/IL-17 induced genes in primary murine hepatocytes. PMID:20374638
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. PMID:20363979
A systems biology approach to transcription factor binding site prediction. PMID:20360861
Comparison of gene expression in hepatocellular carcinoma, liver development, and liver regeneration. PMID:20358383
Variation in transcription factor binding among humans. PMID:20299548
Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data. PMID:20215436
Two frequenins in Drosophila: unveiling the evolutionary history of an unusual neuronal calcium sensor (NCS) duplication. PMID:20170488
Evidence-ranked motif identification. PMID:20156354
Assigning roles to DNA regulatory motifs using comparative genomics. PMID:20147307
A map of open chromatin in human pancreatic islets. PMID:20118932
A novel alignment-free method for comparing transcription factor binding site motifs. PMID:20098703
MicroRNA-145 targets YES and STAT1 in colon cancer cells. PMID:20098684
Cooperative interaction between retinoic acid receptor-alpha and estrogen receptor in breast cancer. PMID:20080953
Genome-wide discovery of human heart enhancers. PMID:20075146
Variable structure motifs for transcription factor binding sites. PMID:20074339
PyMix--the python mixture package--a tool for clustering of heterogeneous biological data. PMID:20053276
Revealing global regulatory perturbations across human cancers. PMID:20005852
Interaction of vitamin D receptor with HLA DRB1 0301 in type 1 diabetes patients from North India. PMID:19956544
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. PMID:19906716
hPDI: a database of experimental human protein-DNA interactions. PMID:19900953
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling. PMID:19879846
Finding distal regulatory elements in the human genome. PMID:19854636
Transcription factor site dependencies in human, mouse and rat genomes. PMID:19835596
Identification of functionally related genes using data mining and data integration: a breast cancer case study. PMID:19828084
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data. PMID:19797408
MicroRNAs regulate osteogenesis and chondrogenesis of mouse bone marrow stromal cells. PMID:19787082
Impact of DNA-binding position variants on yeast gene expression. PMID:19767613
Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. PMID:19767611
Dioxin-dependent and dioxin-independent gene batteries: comparison of liver and kidney in AHR-null mice. PMID:19759094
Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle. PMID:19758441
Temporal induction pattern of STAT4 target genes defines potential for Th1 lineage-specific programming. PMID:19710469
Computational design and application of endogenous promoters for transcriptionally targeted gene therapy for rheumatoid arthritis. PMID:19690516
Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PMID:19668381
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. PMID:19656951
A novel putative miRNA target enhancer signal. PMID:19649282
FISim: a new similarity measure between transcription factor binding sites based on the fuzzy integral. PMID:19615102
Transcriptional programs: modelling higher order structure in transcriptional control. PMID:19607663
Targeted resequencing and analysis of the Diamond-Blackfan anemia disease locus RPS19. PMID:19587786
An integrated genome screen identifies the Wnt signaling pathway as a major target of WT1. PMID:19549856
Death-associated protein 3 is overexpressed in human thyroid oncocytic tumours. PMID:19536094
Identifying regulatory elements in eukaryotic genomes. PMID:19498043
Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays. PMID:19487241
Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP. PMID:19451166
Analytical methods for inferring functional effects of single base pair substitutions in human cancers. PMID:19434427
MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. PMID:19409082
Transcriptional network of p63 in human keratinocytes. PMID:19390658
KIRMES: kernel-based identification of regulatory modules in euchromatic sequences. PMID:19389732
Conservation of core gene expression in vertebrate tissues. PMID:19371447
Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. PMID:19329064
TFCat: the curated catalog of mouse and human transcription factors. PMID:19284633
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. PMID:19265799
COTRASIF: conservation-aided transcription-factor-binding site finder. PMID:19264796
Transcription factor binding sites are genetic determinants of retroviral integration in the human genome. PMID:19238208
DNA motif alignment by evolving a population of Markov chains. PMID:19208112
Expression of the multiple sclerosis-associated MHC class II Allele HLA-DRB1*1501 is regulated by vitamin D. PMID:19197344
Mef2-mediated transcription of the miR379-410 cluster regulates activity-dependent dendritogenesis by fine-tuning Pumilio2 protein levels. PMID:19197241
GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. PMID:19193149
A primer on regression methods for decoding cis-regulatory logic. PMID:19180174
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. PMID:19151087
A transcription factor affinity-based code for mammalian transcription initiation. PMID:19141595
Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence. PMID:19135437
ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. PMID:19118200
Pseudocounts for transcription factor binding sites. PMID:19106141
PASTAA: identifying transcription factors associated with sets of co-regulated genes. PMID:19073590
Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva. PMID:19055776
The C proteins of human parainfluenza virus type 1 (HPIV1) control the transcription of a broad array of cellular genes that would otherwise respond to HPIV1 infection. PMID:19052086
A composite intronic element directs dynamic binding of the progesterone receptor and GATA-2. PMID:19036901
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. PMID:19036138
CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes. PMID:19036135
MotifMap: a human genome-wide map of candidate regulatory motif sites. PMID:19017655
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation. PMID:19014636
Interferon-gamma is a critical modulator of CB(2) cannabinoid receptor signaling during neuropathic pain. PMID:19005078
PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. PMID:18981473
Multigenome DNA sequence conservation identifies Hox cis-regulatory elements. PMID:18981268
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PMID:18974828
An in silico strategy identified the target gene candidates regulated by dehydration responsive element binding proteins (DREBs) in Arabidopsis genome. PMID:18931920
Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases. PMID:18842138
STIF: Identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana. PMID:18841238
Sustained NF-kappaB activation produces a short-term cell proliferation block in conjunction with repressing effectors of cell cycle progression controlled by E2F or FoxM1. PMID:18803232
Transcriptomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in liver: comparison of rat and mouse. PMID:18796159
A feature-based approach to modeling protein-DNA interactions. PMID:18725950
Determining significance of pairwise co-occurrences of events in bursty sequences. PMID:18691400
Recent computational approaches to understand gene regulation: mining gene regulation in silico. PMID:18660846
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. PMID:18585359
Associating transcription factor-binding site motifs with target GO terms and target genes. PMID:18544606
Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression. PMID:18523562
In silico promoters: modelling of cis-regulatory context facilitates target predictio. PMID:18505473
A novel Bayesian DNA motif comparison method for clustering and retrieval. PMID:18463706
Discovering sequence motifs with arbitrary insertions and deletions. PMID:18437229
CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data. PMID:18411210
Probabilistic inference of transcription factor binding from multiple data sources. PMID:18364997
Identification of direct target genes using joint sequence and expression likelihood with application to DAF-16. PMID:18350157
The Innate Immune Database (IIDB). PMID:18321385
Assessment of composite motif discovery methods. PMID:18302777
fdrMotif: identifying cis-elements by an EM algorithm coupled with false discovery rate control. PMID:18296465
Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia. PMID:18291030
Asap: a framework for over-representation statistics for transcription factor binding sites. PMID:18286180
Markov chain-based promoter structure modeling for tissue-specific expression pattern prediction. PMID:18258700
In silico detection of sequence variations modifying transcriptional regulation. PMID:18208319
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. PMID:18086700
Investigation of miRNA biology by bioinformatic tools and impact of miRNAs in colorectal cancer--regulatory relationship of c-Myc and p53 with miRNAs. PMID:18079974
Efficient and accurate P-value computation for Position Weight Matrices. PMID:18072973
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. PMID:18042645
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. PMID:18006571
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors. PMID:17996093
Reliable prediction of regulator targets using 12 Drosophila genomes. PMID:17989251
TREMOR--a tool for retrieving transcriptional modules by incorporating motif covariance. PMID:17962303
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. PMID:17956628
TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. PMID:17947326
Sequences conserved by selection across mouse and human malaria species. PMID:17937810
Discriminative motif discovery in DNA and protein sequences using the DEME algorithm. PMID:17937785
Genome-wide identification of estrogen receptor alpha-binding sites in mouse liver. PMID:17901129
Molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: insights into TCDD-induced endocrine disruption and reproductive toxicity. PMID:17884332
Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer. PMID:17823307
Molecular portrait of cisplatin induced response in human testis cancer cell lines based on gene expression profiles. PMID:17711579
Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PMID:17708682
Inference of transcriptional regulation using gene expression data from the bovine and human genomes. PMID:17683551
oPOSSUM: integrated tools for analysis of regulatory motif over-representation. PMID:17576675
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. PMID:17567999
MATLIGN: a motif clustering, comparison and matching tool. PMID:17559640
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. PMID:17517777
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. PMID:17506886
STAMP: a web tool for exploring DNA-binding motif similarities. PMID:17478497
Integration of genome and chromatin structure with gene expression profiles to predict c-MYC recognition site binding and function. PMID:17411336
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PMID:17397256
MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs. PMID:17378935
The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. PMID:17362513
Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages. PMID:17360536
Quantifying similarity between motifs. PMID:17324271
Localizing hotspots of antisense transcription. PMID:17284453
Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells. PMID:17267408
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry. PMID:17264128
Statistical significance of cis-regulatory modules. PMID:17241466
Large-scale discovery of promoter motifs in Drosophila melanogaster. PMID:17238282
Tissue-specific regulatory elements in mammalian promoters. PMID:17224917
Analyzing the dose-dependence of the Saccharomyces cerevisiae global transcriptional response to methyl methanesulfonate and ionizing radiation. PMID:17140446
CoMoDis: composite motif discovery in mammalian genomes. PMID:17130158
Inference of splicing regulatory activities by sequence neighborhood analysis. PMID:17121466
BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. PMID:17078876
EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. PMID:17071715
Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees. PMID:17065326
Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT. PMID:17064417
A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. PMID:17053090
A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. PMID:17041233
Experimental validation of predicted mammalian erythroid cis-regulatory modules. PMID:17038566
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. PMID:16998473
Common and divergent immune response signaling pathways discovered in peripheral blood mononuclear cell gene expression patterns in presymptomatic and clinically apparent malaria. PMID:16988231
Coding limits on the number of transcription factors. PMID:16984633
Characterization of binding sites of eukaryotic transcription factors. PMID:16970547
Predicting transcription factor binding sites using local over-representation and comparative genomics. PMID:16945132
Fast index based algorithms and software for matching position specific scoring matrices. PMID:16930469
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. PMID:16880385
Computational identification of transcriptional regulatory elements in DNA sequence. PMID:16855295
CEAS: cis-regulatory element annotation system. PMID:16845068
TFBScluster web server for the identification of mammalian composite regulatory elements. PMID:16845063
MEME: discovering and analyzing DNA and protein sequence motifs. PMID:16845028
Biological code breaking in the 21st century. PMID:16738563
Transcription factor map alignment of promoter regions. PMID:16733547
Complex Loci in human and mouse genomes. PMID:16683030
K-SPMM: a database of murine spermatogenic promoters modules & motifs. PMID:16670029
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. PMID:16606704
Transcriptome profile of macrophages from atherosclerosis-sensitive and atherosclerosis-resistant mice. PMID:16518689
Alternative promoter usage of the membrane glycoprotein CD36. PMID:16515687
Regulation of the human LAT gene by the Elf-1 transcription factor. PMID:16464244
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles. PMID:16449500
Foot differentiation and genomic plasticity in Hydra: lessons from the PPOD gene family. PMID:16402271
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. PMID:16381983
HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites. PMID:16381982
DBD: a transcription factor prediction database. PMID:16381970
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. PMID:16381947
DBTGR: a database of tunicate promoters and their regulatory elements. PMID:16381930
The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. PMID:16356267
Measuring similarities between transcription factor binding sites. PMID:16191190
Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions. PMID:16186128
Glucocorticoid receptor-dependent gene regulatory networks. PMID:16110340
Framework for kernel regularization with application to protein clustering. PMID:16109767
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. PMID:16024817
Complex HTR2C linkage disequilibrium and promoter associations with body mass index and serum leptin. PMID:16021472
Dcode.org anthology of comparative genomic tools. PMID:15980535
CONREAL web server: identification and visualization of conserved transcription factor binding sites. PMID:15980509
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. PMID:15980508
T-Reg Comparator: an analysis tool for the comparison of position weight matrices. PMID:15980506
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. PMID:15980497
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. PMID:15933209
Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements. PMID:15930494
De novo cis-regulatory module elicitation for eukaryotic genomes. PMID:15883375
Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals. PMID:15882449
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. PMID:15799782
Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome. PMID:15774015
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. PMID:15760844
Identification of functional SNPs in the 5-prime flanking sequences of human genes. PMID:15717931
Identifying tissue-selective transcription factor binding sites in vertebrate promoters. PMID:15668401
Inferring combinatorial regulation of transcription in silico. PMID:15647509
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. PMID:15608292
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. PMID:15608156
Lower rate of genomic variation identified in the trans-membrane domain of monoamine sub-class of Human G-Protein Coupled Receptors: the Human GPCR-DB Database. PMID:15579207
Decoding human regulatory circuits. PMID:15466295
Bipartite pattern discovery by entropy minimization-based multiple local alignment. PMID:15388800
CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. PMID:15297614
MotifViz: an analysis and visualization tool for motif discovery. PMID:15215422
ConSite: web-based prediction of regulatory elements using cross-species comparison. PMID:15215389
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. PMID:15215387
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. PMID:15215383
MSCAN: identification of functional clusters of transcription factor binding sites. PMID:15215379
Variants of CYP46A1 may interact with age and APOE to influence CSF Abeta42 levels in Alzheimer's disease. PMID:15034781
Detection of functional DNA motifs via statistical over-representation. PMID:14988425
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles PubMed citations: 556.

556 articles citing: JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

TRmir: A Comprehensive Resource for Human Transcriptional Regulatory Information of MiRNAs. PMID:35186035
Retrogene survival is not impacted by linkage relationships. PMID:35127291
Hypermethylation of miR-145 promoter-mediated SOX9-CLDN8 pathway regulates intestinal mucosal barrier in Crohn's disease. PMID:35124427
ARMC Subfamily: Structures, Functions, Evolutions, Interactions, and Diseases. PMID:34912852
LncRNA Hmrhl regulates expression of cancer related genes in chronic myelogenous leukemia through chromatin association. PMID:34734184
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse. PMID:34718747
Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform. PMID:34712617
Pri smORF Peptides Are Wide Mediators of Ecdysone Signaling, Contributing to Shape Spatiotemporal Responses. PMID:34527021
DNA methylome profiling reveals epigenetic regulation of lipoprotein-associated phospholipase A2 in human vulnerable atherosclerotic plaque. PMID:34419168
Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences. PMID:34399797
CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication. PMID:34331449
Loss of RANBP3L leads to transformation of renal epithelial cells towards a renal clear cell carcinoma like phenotype. PMID:34233711
High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites. PMID:34099689
Impacts of the SOAT1 genetic variants and protein expression on HBV-related hepatocellular carcinoma. PMID:34039309
VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics. PMID:33893273
A KRAS-responsive long non-coding RNA controls microRNA processing. PMID:33795683
A Functional Variant rs3093023 in CCR6 Is Associated With IgA Nephropathy by Regulating Th17 Cells in a North Han Chinese Population. PMID:33717080
Suprabasin-A Review. PMID:33477529
Hypoxia-induced FOXO4/LDHA axis modulates gastric cancer cell glycolysis and progression. PMID:33463054
Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. PMID:33304457
LINC01235-TWIST2 feedback loop facilitates epithelial-mesenchymal transition in gastric cancer by inhibiting THBS2. PMID:33206629
Identification of Prognostic Markers in Cholangiocarcinoma Using Altered DNA Methylation and Gene Expression Profiles. PMID:33193605
Identification of Novel Potential Type 2 Diabetes Genes Mediating β-Cell Loss and Hyperglycemia Using Positional Cloning. PMID:33133152
Yes-associated protein (YAP) induces a secretome phenotype and transcriptionally regulates plasminogen activator Inhibitor-1 (PAI-1) expression in hepatocarcinogenesis. PMID:33097058
Progesterone Receptor Signaling Selectively Modulates Cytokine-Induced Global Gene Expression in Human Cervical Stromal Cells. PMID:33061933
Heme-Peroxidase 2, a Peroxinectin-Like Gene, Regulates Bacterial Homeostasis in Anopheles stephensi Midgut. PMID:33013485
Adipocytes fail to maintain cellular identity during obesity due to reduced PPARγ activity and elevated TGFβ-SMAD signaling. PMID:32992037
High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death. PMID:32926651
In silico characterization of synthetic promoters designed from mirabilis mosaic virus and rice tungro bacilliform virus. PMID:32904869
Oncogenic AURKA-enhanced N6-methyladenosine modification increases DROSHA mRNA stability to transactivate STC1 in breast cancer stem-like cells. PMID:32859993
Nucleosome allostery in pioneer transcription factor binding. PMID:32778600
Hypomethylation Causes MIR21 Overexpression in Tumors. PMID:32637580
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Characterization of super-enhancer-associated functional lncRNAs acting as ceRNAs in ESCC. PMID:32460441
Unblending of Transcriptional Condensates in Human Repeat Expansion Disease. PMID:32386547
Immunity-related GTPase induces lipophagy to prevent excess hepatic lipid accumulation. PMID:32376415
Redox-mediated regulation of aging and healthspan by an evolutionarily conserved transcription factor HLH-2/Tcf3/E2A. PMID:32203922
Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement. PMID:32194972
Glycosylation of immunoglobulin G is regulated by a large network of genes pleiotropic with inflammatory diseases. PMID:32128391
S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data. PMID:32086521
Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes. PMID:32085702
Regenerative lineages and immune-mediated pruning in lung cancer metastasis. PMID:32042191
DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD. PMID:32020675
HD-ZIP I Transcription Factor (PtHB13) Negatively Regulates Citrus Flowering through Binding to FLOWERING LOCUS C Promoter. PMID:31963238
rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression. PMID:31928966
Caudal-dependent cell positioning directs morphogenesis of the C. elegans ventral epidermis. PMID:31923384
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. PMID:31913281
Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains. PMID:31910870
The structural basis for cohesin-CTCF-anchored loops. PMID:31905366
NicheNet: modeling intercellular communication by linking ligands to target genes. PMID:31819264
Highly efficient CRISPR-targeting of the murine Hipp11 intergenic region supports inducible human transgene expression. PMID:31811500
TGFB1-Mediated Gliosis in Multiple Sclerosis Spinal Cords Is Favored by the Regionalized Expression of HOXA5 and the Age-Dependent Decline in Androgen Receptor Ligands. PMID:31779094
Evolutionary Dynamics of the SKN-1 → MED → END-1,3 Regulatory Gene Cascade in Caenorhabditis Endoderm Specification. PMID:31740453
Glucocorticoids potentiate the inhibitory capacity of programmed cell death 1 by up-regulating its expression on T cells. PMID:31723031
'One DB to rule them all'-the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs. PMID:31682269
LSD1-mediated repression of GFI1 super-enhancer plays an essential role in erythroleukemia. PMID:31676828
Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. PMID:31666694
A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome. PMID:31649282
Two novel ligand-independent variants of the VEGFR-1 receptor are expressed in human testis and spermatozoa, one of them with the ability to activate SRC proto-oncogene tyrosine kinases. PMID:31645906
IRF2 is a master regulator of human keratinocyte stem cell fate. PMID:31611556
Increased expression of anion transporter SLC26A9 delays diabetes onset in cystic fibrosis. PMID:31581148
Distinct Roles for BET Family Members in Estrogen Receptor α Enhancer Function and Gene Regulation in Breast Cancer Cells. PMID:31551256
Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation. PMID:31519520
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities. PMID:31510640
Residual apoptotic activity of a tumorigenic p53 mutant improves cancer therapy responses. PMID:31483066
Fasting unmasks differential fat and muscle transcriptional regulation of metabolic gene sets in low versus normal birth weight men. PMID:31439477
Cannabinoid CB2 Receptor Modulation by the Transcription Factor NRF2 is Specific in Microglial Cells. PMID:31385133
Investigation of the variants at the binding site of inflammatory transcription factor NF-κB in patients with end-stage renal disease. PMID:31382928
Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation. PMID:31307522
Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient. PMID:31216356
A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reesei. PMID:31213522
Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity. PMID:31202577
Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks. PMID:31159744
Accurate prediction of boundaries of high resolution topologically associated domains (TADs) in fruit flies using deep learning. PMID:31049567
Tissue-specific sex differences in human gene expression. PMID:31044242
SEanalysis: a web tool for super-enhancer associated regulatory analysis. PMID:31028388
Recursive Motif Analyses Identify Brain Epigenetic Transcription Regulatory Modules. PMID:31011409
Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data. PMID:31009236
Temozolomide Treatment Induces lncRNA MALAT1 in an NF-κB and p53 Codependent Manner in Glioblastoma. PMID:30940658
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis. PMID:30931480
DNA-protein interaction: identification, prediction and data analysis. PMID:30915687
Characterization of an HPV33 natural variant with enhanced transcriptional activity suggests a role for C/EBPβ in the regulation of the viral early promoter. PMID:30911096
RECAP reveals the true statistical significance of ChIP-seq peak calls. PMID:30824903
Identification of transcription factor binding sites using ATAC-seq. PMID:30808370
Characterization of DNA Methylation Associated Gene Regulatory Networks During Stomach Cancer Progression. PMID:30778372
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks. PMID:30760546
Synergistic activation of the NEU4 promoter by p73 and AP2 in colon cancer cells. PMID:30700826
High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity. PMID:30683753
The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease. PMID:30645971
Release of transcriptional repression via ErbB2-induced, SUMO-directed phosphorylation of myeloid zinc finger-1 serine 27 activates lysosome redistribution and invasion. PMID:30622337
Atypical β-S haplotypes: classification and genetic modulation in patients with sickle cell anemia. PMID:30622282
Arid3a regulates nephric tubule regeneration via evolutionarily conserved regeneration signal-response enhancers. PMID:30616715
Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPSC reprogramming. PMID:30577748
A Novel Angiotensin II-Induced Long Noncoding RNA Giver Regulates Oxidative Stress, Inflammation, and Proliferation in Vascular Smooth Muscle Cells. PMID:30566058
Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids. PMID:30563463
Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9. PMID:30552336
atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding. PMID:30534948
A new sequence logo plot to highlight enrichment and depletion. PMID:30526486
GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis. PMID:30524706
Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia. PMID:30503705
TFforge utilizes large-scale binding site divergence to identify transcriptional regulators involved in phenotypic differences. PMID:30496469
Alcohol Activates Scabrous-Notch to Influence Associated Memories. PMID:30482693
Zebrafish miR-462-731 regulates hematopoietic specification and pu.1-dependent primitive myelopoiesis. PMID:30459392
Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors. PMID:30359306
atSNPInfrastructure, a case study for searching billions of records while providing significant cost savings over cloud providers. PMID:30349760
An integrative tissue-network approach to identify and test human disease genes. PMID:30346941
Systematic identification and analysis of dysregulated miRNA and transcription factor feed-forward loops in hypertrophic cardiomyopathy. PMID:30338905
The genetic basis of a social polymorphism in halictid bees. PMID:30337532
Recurrent Neural Network for Predicting Transcription Factor Binding Sites. PMID:30323198
Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals. PMID:30289877
IL-6 augments IL-4-induced polarization of primary human macrophages through synergy of STAT3, STAT6 and BATF transcription factors. PMID:30288360
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PMID:30286077
Targeting nuclear receptor NR4A1-dependent adipocyte progenitor quiescence promotes metabolic adaptation to obesity. PMID:30277475
Opaque-2 Regulates a Complex Gene Network Associated with Cell Differentiation and Storage Functions of Maize Endosperm. PMID:30262552
REforge Associates Transcription Factor Binding Site Divergence in Regulatory Elements with Phenotypic Differences between Species. PMID:30256993
Transcriptome profiling of the cardiac neural crest reveals a critical role for MafB. PMID:30236445
Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli. PMID:30089658
STAT3 signaling stimulates miR-21 expression in bovine cumulus cells during in vitro oocyte maturation. PMID:30068990
Species-Specific Changes in a Primate Transcription Factor Network Provide Insights into the Molecular Evolution of the Primate Prefrontal Cortex. PMID:30059966
Functional characteristics of novel pancreatic Pax6 regulatory elements. PMID:30007277
Positional specificity of different transcription factor classes within enhancers. PMID:29987030
Transcription factor NFE2L2/NRF2 modulates chaperone-mediated autophagy through the regulation of LAMP2A. PMID:29950142
Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data. PMID:29940789
In Vivo and In Vitro Neuronal Plasticity Modulation by Epigenetic Regulators. PMID:29931501
Motifome comparison between modern human, Neanderthal and Denisovan. PMID:29914355
Modeling circadian variability of core-clock and clock-controlled genes in four tissues of the rat. PMID:29894471
From genome-wide associations to candidate causal variants by statistical fine-mapping. PMID:29844615
Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli. PMID:29764390
Identification of Novel Functional Variants of SIN3A and SRSF1 among Somatic Variants in Acute Myeloid Leukemia Patients. PMID:29764005
LncRNA PVT1 regulates triple-negative breast cancer through KLF5/beta-catenin signaling. PMID:29760406
An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder. PMID:29703944
Telobox motifs recruit CLF/SWN-PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis. PMID:29700471
Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry. PMID:29695722
TransAtlasDB: an integrated database connecting expression data, metadata and variants. PMID:29688361
The redox-sensing gene Nrf2 affects intestinal homeostasis, insecticide resistance, and Zika virus susceptibility in the mosquito Aedes aegypti. PMID:29685890
INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow-leafed lupin (Lupinus angustifolius L.). PMID:29677403
Selection on the regulation of sympathetic nervous activity in humans and chimpanzees. PMID:29672586
Warming Induces Significant Reprogramming of Beige, but Not Brown, Adipocyte Cellular Identity. PMID:29657031
Evaluation of Animal Models by Comparison with Human Late-Onset Alzheimer's Disease. PMID:29656362
Pro-inflammatory cytokines activate hypoxia-inducible factor 3α via epigenetic changes in mesenchymal stromal/stem cells. PMID:29643458
Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa. PMID:29642851
Gene Duplication and Transference of Function in the paleoAP3 Lineage of Floral Organ Identity Genes. PMID:29628932
TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. PMID:29621972
Transcriptional regulatory networks underlying gene expression changes in Huntington's disease. PMID:29581148
Computational modeling suggests impaired interactions between NKX2.5 and GATA4 in individuals carrying a novel pathogenic D16N NKX2.5 mutation. PMID:29568389
SEASTAR: systematic evaluation of alternative transcription start sites in RNA. PMID:29546410
Dissecting super-enhancer hierarchy based on chromatin interactions. PMID:29507293
A unified approach for quantifying and interpreting DNA shape readout by transcription factors. PMID:29472273
MS AHI1 genetic risk promotes IFNγ+ CD4+ T cells. PMID:29379820
Network analysis of SRC-1 reveals a novel transcription factor hub which regulates endocrine resistant breast cancer. PMID:29367763
Evolutionary Rewiring of Human Regulatory Networks by Waves of Genome Expansion. PMID:29357977
Genome-Wide Methylation Patterns in Androgen-Independent Prostate Cancer Cells: A Comprehensive Analysis Combining MeDIP-Bisulfite, RNA, and microRNA Sequencing Data. PMID:29324665
Insights into teleost sex determination from the Seriola dorsalis genome assembly. PMID:29310588
Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers. PMID:29301499
MicroRNA-221-3p, a TWIST2 target, promotes cervical cancer metastasis by directly targeting THBS2. PMID:29242498
Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules. PMID:29229750
STAT3 controls COL1A2 enhancer activation cooperatively with JunB, regulates type I collagen synthesis posttranscriptionally, and is essential for lung myofibroblast differentiation. PMID:29142074
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. PMID:29140473
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. PMID:29140464
An empirical Bayes test for allelic-imbalance detection in ChIP-seq. PMID:29126153
Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation. PMID:29123983
Hippo, TGF-β, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection. PMID:29108021
A functional strategy to characterize expression Quantitative Trait Loci. PMID:29101457
High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells. PMID:29101361
Cancer cell line specific co-factors modulate the FOXM1 cistrome. PMID:29100329
The zebrafish miR-125c is induced under hypoxic stress via hypoxia-inducible factor 1α and functions in cellular adaptations and embryogenesis. PMID:29088751
APC downregulated 1 inhibits breast cancer cell invasion by inhibiting the canonical WNT signaling pathway. PMID:29085490
Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis. PMID:29074988
A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. PMID:29056226
Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8+ T Cells in Chronic versus Acute Infection. PMID:29045899
Impairment of IGF2 gene expression in prostate cancer is triggered by epigenetic dysregulation of IGF2-DMR0 and its interaction with KLF4. PMID:29017567
The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies. PMID:28982128
Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling. PMID:28981893
In silico design of context-responsive mammalian promoters with user-defined functionality. PMID:28977454
Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia. PMID:28977425
NCoR1-independent mechanism plays a role in the action of the unliganded thyroid hormone receptor. PMID:28923959
MYC-dependent recruitment of RUNX1 and GATA2 on the SET oncogene promoter enhances PP2A inactivation in acute myeloid leukemia. PMID:28903318
Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. PMID:28893714
Sex-based differences in myocardial gene expression in recently deceased organ donors with no prior cardiovascular disease. PMID:28850583
Population genetics of IFITM3 in Portugal and Central Africa reveals a potential modifier of influenza severity. PMID:28842783
Auxin Response Factor Genes Repertoire in Mulberry: Identification, and Structural, Functional and Evolutionary Analyses. PMID:28841197
Super-lncRNAs: identification of lncRNAs that target super-enhancers via RNA:DNA:DNA triplex formation. PMID:28839111
Modelling the evolution of transcription factor binding preferences in complex eukaryotes. PMID:28790414
Annotation Regression for Genome-Wide Association Studies with an Application to Psychiatric Genomic Consortium Data. PMID:28781711
β1-Integrin Deletion From the Lens Activates Cellular Stress Responses Leading to Apoptosis and Fibrosis. PMID:28763805
Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum. PMID:28747644
MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics. PMID:28738873
Genome Organization Drives Chromosome Fragility. PMID:28735753
Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis. PMID:28717181
Short DNA sequence patterns accurately identify broadly active human enhancers. PMID:28716036
A sequence level model of an intact locus predicts the location and function of nonadditive enhancers. PMID:28715438
GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis. PMID:28695067
Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. PMID:28691125
Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting. PMID:28659711
IRF6 Regulates Alternative Activation by Suppressing PPARγ in Male Murine Macrophages. PMID:28645193
A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a. PMID:28642491
WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data. PMID:28607381
PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. PMID:28607179
Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis. PMID:28605770
RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. PMID:28591841
Modeling the cis-regulatory modules of genes expressed in developmental stages of Drosophila melanogaster. PMID:28584716
Common variants upstream of MLF1 at 3q25 and within CPZ at 4p16 associated with neuroblastoma. PMID:28545128
Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees. PMID:28542163
GLANET: genomic loci annotation and enrichment tool. PMID:28541490
OsPhyB-Mediating Novel Regulatory Pathway for Drought Tolerance in Rice Root Identified by a Global RNA-Seq Transcriptome Analysis of Rice Genes in Response to Water Deficiencies. PMID:28491065
TCF21 and the environmental sensor aryl-hydrocarbon receptor cooperate to activate a pro-inflammatory gene expression program in coronary artery smooth muscle cells. PMID:28481916
The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension. PMID:28475897
Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom. PMID:28429538
Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer. PMID:28423671
Epo reprograms the epigenome of erythroid cells. PMID:28410882
Characterizing Genetic Susceptibility to Breast Cancer in Women of African Ancestry. PMID:28377418
The Zic family homologue Odd-paired regulates Alk expression in Drosophila. PMID:28369060
Dynamic Gene Regulatory Networks of Human Myeloid Differentiation. PMID:28365152
Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus. PMID:28348391
Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease. PMID:28335003
GWAS identifies population-specific new regulatory variants in FUT6 associated with plasma B12 concentrations in Indians. PMID:28334792
Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk prediction. PMID:28262806
Imputation for transcription factor binding predictions based on deep learning. PMID:28234893
Abnormal epigenetic changes during differentiation of human skeletal muscle stem cells from obese subjects. PMID:28222718
Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. PMID:28218758
Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster. PMID:28218276
A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation. PMID:28213474
DNA methylation of the Fthl17 5'-upstream region regulates differential Fthl17 expression in lung cancer cells and germline stem cells. PMID:28207785
CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data. PMID:28204599
Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast. PMID:28158860
Critical role of the cAMP-PKA pathway in hyperglycemia-induced epigenetic activation of fibrogenic program in the kidney. PMID:28148567
Systematic dissection of genomic features determining transcription factor binding and enhancer function. PMID:28137873
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. PMID:28126036
Identification of a Nuclear Respiratory Factor 1 Recognition Motif in the Apolipoprotein E Variant APOE4 linked to Alzheimer's Disease. PMID:28094792
Genome-wide analysis of p53-regulated transcription in Myc-driven lymphomas. PMID:28092679
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. PMID:28072816
Breast Cancer Malignant Processes are Regulated by Pax-5 Through the Disruption of FAK Signaling Pathways. PMID:28070224
Identification of coding and non-coding mutational hotspots in cancer genomes. PMID:28056774
Optimized logic rules reveal interferon-γ-induced modes regulated by histone deacetylases and protein tyrosine phosphatases. PMID:28054346
Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation. PMID:28049421
Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies. PMID:28044063
Androgen receptor transcriptionally regulates semaphorin 3C in a GATA2-dependent manner. PMID:28038451
Foxo4- and Stat3-dependent IL-10 production by progranulin in regulatory T cells restrains inflammatory arthritis. PMID:28011648
The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. PMID:27992400
Quantifying deleterious effects of regulatory variants. PMID:27980060
Effective Feature Selection for Classification of Promoter Sequences. PMID:27978541
The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences. PMID:27934697
Zinc Cluster Transcription Factors Alter Virulence in Candida albicans. PMID:27932543
PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c. PMID:27932482
Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity. PMID:27932399
OTX2 impedes self-renewal of porcine iPS cells through downregulation of NANOG expression. PMID:27924227
Overexpression of AtEDT1 promotes root elongation and affects medicinal secondary metabolite biosynthesis in roots of transgenic Salvia miltiorrhiza. PMID:27915455
IL-10 production by CLL cells is enhanced in the anergic IGHV mutated subset and associates with reduced DNA methylation of the IL10 locus. PMID:27890932
Gene regulatory networks in neural cell fate acquisition from genome-wide chromatin association of Geminin and Zic1. PMID:27881878
A Herpesviral induction of RAE-1 NKG2D ligand expression occurs through release of HDAC mediated repression. PMID:27874833
Actin is an evolutionarily-conserved damage-associated molecular pattern that signals tissue injury in Drosophila melanogaster. PMID:27871362
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. PMID:27871221
YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. PMID:27857184
Feature-based classification of human transcription factors into hypothetical sub-classes related to regulatory function. PMID:27842491
Integrated computational approach to the analysis of RNA-seq data reveals new transcriptional regulators of psoriasis. PMID:27811935
Evaluating tools for transcription factor binding site prediction. PMID:27806697
Most brain disease-associated and eQTL haplotypes are not located within transcription factor DNase-seq footprints in brain. PMID:27798116
Large Scale Gene Expression Meta-Analysis Reveals Tissue-Specific, Sex-Biased Gene Expression in Humans. PMID:27790248
Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia. PMID:27782217
A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions. PMID:27777270
Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations. PMID:27768888
An Intronic Enhancer Element Regulates Angiotensin II Type 2 Receptor Expression during Satellite Cell Differentiation, and Its Activity Is Suppressed in Congestive Heart Failure. PMID:27756842
Associations of the calcium-sensing receptor gene CASR rs7652589 SNP with nephrolithiasis and secondary hyperparathyroidism in haemodialysis patients. PMID:27739473
Activation of Ftz-F1-Responsive Genes through Ftz/Ftz-F1 Dependent Enhancers. PMID:27723822
Computational identification of putative lincRNAs in mouse embryonic stem cell. PMID:27713513
Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate. PMID:27710791
Identification of Position-Specific Correlations between DNA-Binding Domains and Their Binding Sites. Application to the MerR Family of Transcription Factors. PMID:27690309
Prediction and validation of protein-protein interactors from genome-wide DNA-binding data using a knowledge-based machine-learning approach. PMID:27683156
Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors. PMID:27658967
The application of transcriptomic data in the authentication of beef derived from contrasting production systems. PMID:27654331
CardioTF, a database of deconstructing transcriptional circuits in the heart system. PMID:27635320
Identification of Pathway-Specific Serum Biomarkers of Response to Glucocorticoid and Infliximab Treatment in Children with Inflammatory Bowel Disease. PMID:27628422
Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines. PMID:27623747
Investigating regulatory signatures of human autophagy related gene 5 (ATG5) through functional in silico analysis. PMID:27617225
Polymorphism within a Neuronal Activity-Dependent Enhancer of NgR1 Is Associated with Corpus Callosum Morphology in Humans. PMID:27602360
Unbiased identification of signal-activated transcription factors by barcoded synthetic tandem repeat promoter screening (BC-STAR-PROM). PMID:27601530
Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis. PMID:27588814
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA). PMID:27585267
Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome. PMID:27565349
PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina. PMID:27556059
DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo. PMID:27546793
Investigating the Molecular Basis of PPCD3: Characterization of ZEB1 Regulation of COL4A3 Expression. PMID:27537263
Cross-species Conservation of context-specific networks. PMID:27531214
Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa. PMID:27524493
Linking Core Promoter Classes to Circadian Transcription. PMID:27504829
Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants. PMID:27503086
Modeling protein-DNA binding via high-throughput in vitro technologies. PMID:27497616
Evaluating the impact of single nucleotide variants on transcription factor binding. PMID:27492288
Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types. PMID:27490693
Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters. PMID:27487356
FAR-RED ELONGATED HYPOCOTYL3 activates SEPALLATA2 but inhibits CLAVATA3 to regulate meristem determinacy and maintenance in Arabidopsis. PMID:27469166
Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. PMID:27468897
Exome-based Variant Detection in Core Promoters. PMID:27464681
A Systems View of the Differences between APOE ε4 Carriers and Non-carriers in Alzheimer's Disease. PMID:27462267
Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. PMID:27458208
Bats: Body mass index, forearm mass index, blood glucose levels and SLC2A2 genes for diabetes. PMID:27439361
Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers. PMID:27436900
Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis. PMID:27426982
TERT promoter mutations in pancreatic endocrine tumours are rare and mainly found in tumours from patients with hereditary syndromes. PMID:27411289
LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome. PMID:27410265
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PMID:27403523
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. PMID:27402679
Association of HOMER1 rs2290639 with suicide attempts in Hong Kong Chinese and the potentially functional role of this polymorphism. PMID:27386253
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Identification of Potentially Pathogenic Variants in the Posterior Polymorphous Corneal Dystrophy 1 Locus. PMID:27355326
A Common CYFIP1 Variant at the 15q11.2 Disease Locus Is Associated with Structural Variation at the Language-Related Left Supramarginal Gyrus. PMID:27351196
Epigenetic Signatures of Salivary Gland Inflammation in Sjögren's Syndrome. PMID:27332624
Androgen receptor transcriptionally regulates μ-opioid receptor expression in rat trigeminal ganglia. PMID:27320211
Structure-based prediction of transcription factor binding specificity using an integrative energy function. PMID:27307632
The Juvenile Phase of Maize Sees Upregulation of Stress-Response Genes and Is Extended by Exogenous Jasmonic Acid. PMID:27307257
Genome-wide characterization of human L1 antisense promoter-driven transcripts. PMID:27301971
RTFBSDB: an integrated framework for transcription factor binding site analysis. PMID:27288497
Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control. PMID:27288492
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. PMID:27288444
Significance of duon mutations in cancer genomes. PMID:27272679
Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing. PMID:27211859
A systematic, large-scale comparison of transcription factor binding site models. PMID:27209209
DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C. PMID:27199372
Interactions between pluripotency factors specify cis-regulation in embryonic stem cells. PMID:27197208
The nitrogen responsive transcriptome in potato (Solanum tuberosum L.) reveals significant gene regulatory motifs. PMID:27193058
Comparison between Timelines of Transcriptional Regulation in Mammals, Birds, and Teleost Fish Somitogenesis. PMID:27192554
Six Tissue Transcriptomics Reveals Specific Immune Suppression in Spleen by Dietary Polyunsaturated Fatty Acids. PMID:27166587
Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information. PMID:27165633
rAAV-compatible MiniPromoters for restricted expression in the brain and eye. PMID:27164903
PPARgene: A Database of Experimentally Verified and Computationally Predicted PPAR Target Genes. PMID:27148361
Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures. PMID:27143130
Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data. PMID:27131787
Positional distribution of transcription factor binding sites in Arabidopsis thaliana. PMID:27117388
Characterization of piRNAs across postnatal development in mouse brain. PMID:27112104
Point Mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. PMID:27087319
Essential role of insulin-like growth factor 2 in resistance to histone deacetylase inhibitors. PMID:27086926
Distinct epigenetic signatures elucidate enhancer-gene relationships that delineate CIMP and non-CIMP colorectal cancers. PMID:27049830
Data- and knowledge-based modeling of gene regulatory networks: an update. PMID:27047314
The retinoblastoma protein regulates hypoxia-inducible genetic programs, tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. PMID:27015368
A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe. PMID:27014338
CTCF-mediated chromatin loops enclose inducible gene regulatory domains. PMID:27004515
Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler. PMID:26993344
Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress. PMID:26990640
STAT4-mediated transcriptional repression of the IL5 gene in human memory Th2 cells. PMID:26990433
Initiation of cyp26a1 Expression in the Zebrafish Anterior Neural Plate by a Novel Cis-Acting Element. PMID:26959238
The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. PMID:26945717
Bidirectional promoters link cAMP signaling with irreversible differentiation through promoter-associated non-coding RNA (pancRNA) expression in PC12 cells. PMID:26945044
Regulatory evolution of innate immunity through co-option of endogenous retroviruses. PMID:26941318
The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs. PMID:26908612
Hyperglycemia and hyperlipidemia blunts the Insulin-Inpp5f negative feedback loop in the diabetic heart. PMID:26908121
Analysis of computational footprinting methods for DNase sequencing experiments. PMID:26901649
A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors. PMID:26896797
Targeted resequencing identifies PTCH1 as a major contributor to ocular developmental anomalies and extends the SOX2 regulatory network. PMID:26893459
Ensembl regulation resources. PMID:26888907
GRHL2-miR-200-ZEB1 maintains the epithelial status of ovarian cancer through transcriptional regulation and histone modification. PMID:26887977
Genomic sequencing of a dyslexia susceptibility haplotype encompassing ROBO1. PMID:26877820
Models of human core transcriptional regulatory circuitries. PMID:26843070
Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development. PMID:26829553
Characterization and Expression of the Lucina pectinata Oxygen and Sulfide Binding Hemoglobin Genes. PMID:26824233
Genetic variations in GPSM3 associated with protection from rheumatoid arthritis affect its transcript abundance. PMID:26821282
Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. PMID:26818008
Knowledge-based three-body potential for transcription factor binding site prediction. PMID:26816396
TFBSTools: an R/bioconductor package for transcription factor binding site analysis. PMID:26794315
Structural Mechanism behind Distinct Efficiency of Oct4/Sox2 Proteins in Differentially Spaced DNA Complexes. PMID:26790000
Assessment of fight outcome is needed to activate socially driven transcriptional changes in the zebrafish brain. PMID:26787876
Microglial brain region-dependent diversity and selective regional sensitivities to aging. PMID:26780511
Transcription factor NFAT1 controls allergic contact hypersensitivity through regulation of activation induced cell death program. PMID:26777750
CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms. PMID:26773058
Mapping nucleosome positions using DNase-seq. PMID:26772197
Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer. PMID:26769127
Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. PMID:26766440
Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements. PMID:26760036
An efficient full-length cDNA amplification strategy based on bioinformatics technology and multiplexed PCR methods. PMID:26758040
Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction. PMID:26721385
Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio). PMID:26713440
Genome-wide identification of hypoxia-induced enhancer regions. PMID:26713262
The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae. PMID:26697386
Irf6 directly regulates Klf17 in zebrafish periderm and Klf4 in murine oral epithelium, and dominant-negative KLF4 variants are present in patients with cleft lip and palate. PMID:26692521
Characterization of marine diatom-infecting virus promoters in the model diatom Phaeodactylum tricornutum. PMID:26692124
Evidence for a common evolutionary rate in metazoan transcriptional networks. PMID:26682651
Differential DNA Methylation Analysis without a Reference Genome. PMID:26673328
Systematic dissection of dysregulated transcription factor-miRNA feed-forward loops across tumor types. PMID:26655252
Liver ChIP-seq analysis in FGF19-treated mice reveals SHP as a global transcriptional partner of SREBP-2. PMID:26634251
Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites. PMID:26628745
Mtss1 is a critical epigenetically regulated tumor suppressor in CML. PMID:26621336
Branched-chain amino acid catabolism is a conserved regulator of physiological ageing. PMID:26620638
Inhibition of Lysyl Oxidases Improves Drug Diffusion and Increases Efficacy of Cytotoxic Treatment in 3D Tumor Models. PMID:26620400
The long noncoding RNA Gm15055 represses Hoxa gene expression by recruiting PRC2 to the gene cluster. PMID:26615201
Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells. PMID:26599758
Modeling co-occupancy of transcription factors using chromatin features. PMID:26590261
Nuclear Factor κB1/RelA Mediates Inflammation in Human Lung Epithelial Cells at Atmospheric Oxygen Levels. PMID:26588041
A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis. PMID:26586835
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. PMID:26586801
DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. PMID:26586797
SEA: a super-enhancer archive. PMID:26578594
ORegAnno 3.0: a community-driven resource for curated regulatory annotation. PMID:26578589
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. PMID:26560027
Iroquois Proteins Promote Skeletal Joint Formation by Maintaining Chondrocytes in an Immature State. PMID:26555055
Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci. PMID:26551672
Nitric Oxide Regulates Gene Expression in Cancers by Controlling Histone Posttranslational Modifications. PMID:26542213
Genome-wide endogenous DAF-16/FOXO recruitment dynamics during lowered insulin signalling in C. elegans. PMID:26539642
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. PMID:26531826
Functionally conserved enhancers with divergent sequences in distant vertebrates. PMID:26519295
MicroRNA Library-Based Functional Screening Identified Androgen-Sensitive miR-216a as a Player in Bicalutamide Resistance in Prostate Cancer. PMID:26506397
Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PMID:26505748
The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection. PMID:26503446
rVarBase: an updated database for regulatory features of human variants. PMID:26503253
A cellular, molecular, and pharmacological basis for appendage regeneration in mice. PMID:26494786
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. PMID:26476450
Differences in the Early Development of Human and Mouse Embryonic Stem Cells. PMID:26473594
Homeodomain proteins: an update. PMID:26464018
Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells. PMID:26459242
Molecular targets of androgen signaling that characterize skeletal muscle recovery and regeneration. PMID:26457071
Functional Analyses of Transcription Factor Binding Sites that Differ between Present-Day and Archaic Humans. PMID:26454764
Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species. PMID:26444262
Alternative transcription initiation leads to expression of a novel ALK isoform in cancer. PMID:26444240
Transcriptional Regulation of Cytosolic Sulfotransferase 1C2 by Intermediates of the Cholesterol Biosynthetic Pathway in Primary Cultured Rat Hepatocytes. PMID:26427720
Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism. PMID:26423458
How to Isolate a Plant's Hypomethylome in One Shot. PMID:26421293
Mechanisms of Soybean Roots' Tolerances to Salinity Revealed by Proteomic and Phosphoproteomic Comparisons Between Two Cultivars. PMID:26407991
De novo ChIP-seq analysis. PMID:26400819
BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates. PMID:26388941
BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. PMID:26375006
Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system. PMID:26369791
Living without DAT: Loss and compensation of the dopamine transporter gene in sauropsids (birds and reptiles). PMID:26364979
A Kelch Domain-Containing F-Box Coding Gene Negatively Regulates Flavonoid Accumulation in Muskmelon. PMID:26358418
The search for cis-regulatory driver mutations in cancer genomes. PMID:26356674
Prosaposin activates the androgen receptor and potentiates resistance to endocrine treatment in breast cancer. PMID:26341737
Lineage, fate, and fate potential of NG2-glia. PMID:26301825
Global Promoter Targeting of a Conserved Lysine Deacetylase for Transcriptional Shutoff during Quiescence Entry. PMID:26300265
Reliable scaling of position weight matrices for binding strength comparisons between transcription factors. PMID:26289072
The A Allele at rs13419896 of EPAS1 Is Associated with Enhanced Expression and Poor Prognosis for Non-Small Cell Lung Cancer. PMID:26263511
Heterogeneous Effects of Direct Hypoxia Pathway Activation in Kidney Cancer. PMID:26262842
Global identification of the genetic networks and cis-regulatory elements of the cold response in zebrafish. PMID:26227973
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. PMID:26213851
Correlation of the osteoarthritis susceptibility variants that map to chromosome 20q13 with an expression quantitative trait locus operating on NCOA3 and with functional variation at the polymorphism rs116855380. PMID:26211391
GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species. PMID:26208093
Motif signatures in stretch enhancers are enriched for disease-associated genetic variants. PMID:26180553
BCR/ABL1 and BCR are under the transcriptional control of the MYC oncogene. PMID:26179066
Beyond antioxidant genes in the ancient Nrf2 regulatory network. PMID:26163000
Antioxidants in Translational Medicine. PMID:26154592
Time-course gene profiling and networks in demethylated retinoblastoma cell line. PMID:26143641
A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes. PMID:26131856
Vitamin D Receptor Gene Ablation in the Conceptus Has Limited Effects on Placental Morphology, Function and Pregnancy Outcome. PMID:26121239
Photosynthetic Genes and Genes Associated with the C4 Trait in Maize Are Characterized by a Unique Class of Highly Regulated Histone Acetylation Peaks on Upstream Promoters. PMID:26111542
Putative regulation mechanism for the MSTN gene by a CpG island generated by the SINE marker Ins227bp. PMID:26100061
atSNP: transcription factor binding affinity testing for regulatory SNP detection. PMID:26092860
By the company they keep: interaction networks define the binding ability of transcription factors. PMID:26089389
Influence of functional polymorphisms in TNF-α, IL-8, and IL-10 cytokine genes on mRNA expression levels and risk of gastric cancer. PMID:26088449
Identification of novel Fgf enhancers and their role in dental evolution. PMID:26086993
The Human Blood Metabolome-Transcriptome Interface. PMID:26086077
Epigenetic modifications of the glucocorticoid receptor gene are associated with the vulnerability to psychopathology in childhood maltreatment. PMID:26080088
Inference of transcriptional regulation in cancers. PMID:26056275
Recurrent somatic mutations in regulatory regions of human cancer genomes. PMID:26053494
Analysis of the transcriptional regulation of cancer-related genes by aberrant DNA methylation of the cis-regulation sites in the promoter region during hepatocyte carcinogenesis caused by arsenic. PMID:26046465
Protein-DNA binding in high-resolution. PMID:26038153
SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps. PMID:26016777
A possible role of Drosophila CTCF in mitotic bookmarking and maintaining chromatin domains during the cell cycle. PMID:26013116
Regulators associated with clinical outcomes revealed by DNA methylation data in breast cancer. PMID:25996148
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. PMID:25994056
A novel DNA sequence motif in human and mouse genomes. PMID:25990515
Constitutive control of AKT1 gene expression by JUNB/CJUN in ALK+ anaplastic large-cell lymphoma: a novel crosstalk mechanism. PMID:25987255
Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. PMID:25984238
Comprehensively evaluating cis-regulatory variation in the human prostate transcriptome by using gene-level allele-specific expression. PMID:25983244
Human Enhancers Are Fragile and Prone to Deactivating Mutations. PMID:25976354
The MEME Suite. PMID:25953851
FNTM: a server for predicting functional networks of tissues in mouse. PMID:25940632
Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data. PMID:25927199
The distal upstream promoter in Ly49 genes, Pro1, is active in mature NK cells and T cells, does not require TATA boxes, and displays enhancer activity. PMID:25926675
The transcriptional cofactor TRIM33 prevents apoptosis in B lymphoblastic leukemia by deactivating a single enhancer. PMID:25919951
Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene. PMID:25918715
Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors. PMID:25918418
Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome. PMID:25908307
Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. PMID:25905672
RSAT 2015: Regulatory Sequence Analysis Tools. PMID:25904632
Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas. PMID:25903198
A property-based analysis of human transcription factors. PMID:25890365
Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data. PMID:25887857
Unraveling the 3D genome: genomics tools for multiscale exploration. PMID:25887733
Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks. PMID:25886852
Methylation-dependent SOX9 expression mediates invasion in human melanoma cells and is a negative prognostic factor in advanced melanoma. PMID:25885555
Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites. PMID:25883770
Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription. PMID:25881024
Molecular development of chondrichthyan claspers and the evolution of copulatory organs. PMID:25868783
In silico analysis of the genes encoding proteins that are involved in the biosynthesis of the RMS/MAX/D pathway revealed new roles of Strigolactones in plants. PMID:25815594
GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PMID:25815464
A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements. PMID:25796517
p53-dependent expression of CXCR5 chemokine receptor in MCF-7 breast cancer cells. PMID:25786345
RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation. PMID:25783031
A glycine insertion in the estrogen-related receptor (ERR) is associated with enhanced expression of three cytochrome P450 genes in transgenic Drosophila melanogaster. PMID:25761142
Genome-wide CIITA-binding profile identifies sequence preferences that dictate function versus recruitment. PMID:25753668
Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PMID:25748510
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples. PMID:25725063
Base-resolution methylation patterns accurately predict transcription factor bindings in vivo. PMID:25722376
Biological databases for human research. PMID:25712261
Identifying transcriptional cis-regulatory modules in animal genomes. PMID:25704908
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. PMID:25697895
A transcriptomic analysis of Neurospora crassa using five major crop residues and the novel role of the sporulation regulator rca-1 in lignocellulase production. PMID:25691917
Gene expression changes during retinal development and rod specification. PMID:25678762
CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. PMID:25653163
A single nucleotide polymorphism associated with isolated cleft lip and palate, thyroid cancer and hypothyroidism alters the activity of an oral epithelium and thyroid enhancer near FOXE1. PMID:25652407
Lagging-strand replication shapes the mutational landscape of the genome. PMID:25624100
The emerging roles of GPRC5A in diseases. PMID:25621293
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles. PMID:25601023
A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. PMID:25593323
Two potential hookworm DAF-16 target genes, SNR-3 and LPP-1: gene structure, expression profile, and implications of a cis-regulatory element in the regulation of gene expression. PMID:25573064
Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins. PMID:25559185
Sex- and tissue-specific functions of Drosophila doublesex transcription factor target genes. PMID:25535918
Next-generation sequencing of genomic DNA fragments bound to a transcription factor in vitro reveals its regulatory potential. PMID:25534860
cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. PMID:25521507
Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. PMID:25477382
Computational approaches to interpreting genomic sequence variation. PMID:25473426
Chromatin accessibility: a window into the genome. PMID:25473421
Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells. PMID:25428352
Regulatory network decoded from epigenomes of surface ectoderm-derived cell types. PMID:25421844
Identification of highly conserved putative developmental enhancers bound by SOX3 in neural progenitors using ChIP-Seq. PMID:25409526
Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injury. PMID:25407019
Oxytocin and vasopressin receptor gene variation as a proximate base for inter- and intraspecific behavioral differences in bonobos and chimpanzees. PMID:25405348
Sustained β-catenin activity in dermal fibroblasts promotes fibrosis by up-regulating expression of extracellular matrix protein-coding genes. PMID:25385294
In silico pooling of ChIP-seq control experiments. PMID:25380244
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. PMID:25378322
Genetic variation of the transthyretin gene in wild-type transthyretin amyloidosis (ATTRwt). PMID:25367359
Genomic mapping of the MHC transactivator CIITA using an integrated ChIP-seq and genetical genomics approach. PMID:25366989
TFClass: a classification of human transcription factors and their rodent orthologs. PMID:25361979
Ensembl 2015. PMID:25352552
Decoding neural transcriptomes and epigenomes via high-throughput sequencing. PMID:25349913
SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences. PMID:25341390
A palindromic motif in the -2084 to -2078 upstream region is essential for ABCA12 promoter function in cultured human keratinocytes. PMID:25338618
The Fusarium graminearum genome reveals more secondary metabolite gene clusters and hints of horizontal gene transfer. PMID:25333987
OncoCis: annotation of cis-regulatory mutations in cancer. PMID:25298093
Functional annotation of putative regulatory elements at cancer susceptibility Loci. PMID:25288875
Integrative post-genome-wide association analysis of CDKN2A and TP53 SNPs and risk of esophageal adenocarcinoma. PMID:25280564
Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression. PMID:25277163
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. PMID:25270877
CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining. PMID:25268582
Defining differential genetic signatures in CXCR4- and the CCR5-utilizing HIV-1 co-linear sequences. PMID:25265194
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. PMID:25209146
MicroRNAs 206 and 21 cooperate to promote RAS-extracellular signal-regulated kinase signaling by suppressing the translation of RASA1 and SPRED1. PMID:25202123
Identification of a face enhancer reveals direct regulation of LIM homeobox 8 (Lhx8) by wingless-int (WNT)/β-catenin signaling. PMID:25190800
EZH2 modulates angiogenesis in vitro and in a mouse model of limb ischemia. PMID:25189741
Differential motif enrichment analysis of paired ChIP-seq experiments. PMID:25179504
DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells. PMID:25161698
A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster. PMID:25153327
Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain. PMID:25145340
Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C. PMID:25122612
Haematopoietic stem cell induction by somite-derived endothelial cells controlled by meox1. PMID:25119043
A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL. PMID:25114055
The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. PMID:25106871
Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3. PMID:25053427
High-throughput functional testing of ENCODE segmentation predictions. PMID:25035418
The functional significance of common polymorphisms in zinc finger transcription factors. PMID:24970883
On the identification of potential regulatory variants within genome wide association candidate SNP sets. PMID:24920305
Integrative transcriptome meta-analysis reveals widespread sex-biased gene expression at the human fetal-maternal interface. PMID:24867328
Molecular architecture of transcription factor hotspots in early adipogenesis. PMID:24857666
MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF-β/BMP signaling. PMID:24802670
DMINDA: an integrated web server for DNA motif identification and analyses. PMID:24753419
Mutual enrichment in ranked lists and the statistical assessment of position weight matrix motifs. PMID:24708618
FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. PMID:24658142
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. PMID:24316579
TFBSshape: a motif database for DNA shape features of transcription factor binding sites. PMID:24214955
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles PubMed citations: 528.

528 articles citing: JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

A Quartet Network Analysis Identifying Mechanically Responsive Long Noncoding RNAs in Bone Remodeling. PMID:35356768
Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. PMID:35269428
Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene. PMID:35212624
The Cumulative Formation of R-loop Interacts with Histone Modifications to Shape Cell Reprogramming. PMID:35163490
Human transcription factor protein interaction networks. PMID:35140242
Functional Deletion/Insertion Promoter Variants in SCARB1 Associated With Increased Susceptibility to Lipid Profile Abnormalities and Coronary Heart Disease. PMID:35097019
SOX2 mediates metabolic reprogramming of prostate cancer cells. PMID:35067686
Associations between the Levels of Estradiol-, Progesterone-, and Testosterone-Sensitive MiRNAs and Main Clinicopathologic Features of Breast Cancer. PMID:35055320
Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis. PMID:35045977
Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis. PMID:35013308
Cinnamaldehyde prevents intergenerational effect of paternal depression in mice via regulating GR/miR-190b/BDNF pathway. PMID:34983931
SNHG15 is a negative regulator of inflammation by mediating TRAF2 ubiquitination in stroke-induced immunosuppression. PMID:34980176
Delilah, prospero, and D-Pax2 constitute a gene regulatory network essential for the development of functional proprioceptors. PMID:34964712
Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors. PMID:34789735
Klf5 establishes bi-potential cell fate by dual regulation of ICM and TE specification genes. PMID:34758315
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. PMID:34755879
Major Reorganization of Chromosome Conformation During Muscle Development in Pig. PMID:34675966
NeuroD1 promotes tumor cell proliferation and tumorigenesis by directly activating the pentose phosphate pathway in colorectal carcinoma. PMID:34657129
Hominini-specific regulation of CBLN2 increases prefrontal spinogenesis. PMID:34599306
Synthetic essentiality between PTEN and core dependency factor PAX7 dictates rhabdomyosarcoma identity. PMID:34535684
Autophagy-mediated negative feedback attenuates the oncogenic activity of YAP in pancreatic cancer. PMID:34512171
Skeletal muscle-targeted delivery of Fgf6 protects mice from diet-induced obesity and insulin resistance. PMID:34491915
Targeting of eIF6-driven translation induces a metabolic rewiring that reduces NAFLD and the consequent evolution to hepatocellular carcinoma. PMID:34385447
Topological isolation of developmental regulators in mammalian genomes. PMID:34385432
Improving representations of genomic sequence motifs in convolutional networks with exponential activations. PMID:34322657
Functional annotation of noncoding mutations in cancer. PMID:34282050
STAT3-Dependent Gene TRIM5γ Interacts With HBx Through a Zinc Binding Site on the BBox Domain. PMID:34276596
Simultaneous deep generative modeling and clustering of single cell genomic data. PMID:34179690
The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination. PMID:34174187
Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. PMID:34159315
lncRNA GAS6-AS1 inhibits progression and glucose metabolism reprogramming in LUAD via repressing E2F1-mediated transcription of GLUT1. PMID:34141461
The stabilization of yes-associated protein by TGFβ-activated kinase 1 regulates the self-renewal and oncogenesis of gastric cancer stem cells. PMID:34075691
Cell-type-specific effects of genetic variation on chromatin accessibility during human neuronal differentiation. PMID:34017130
Cardiac cell type-specific gene regulatory programs and disease risk association. PMID:33990324
A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages. PMID:33976173
Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens. PMID:33927415
Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia. PMID:33911178
Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells. PMID:33909924
Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends. PMID:33903630
Predicted regulatory SNPs reveal potential drug targets and novel companion diagnostics in psoriasis. PMID:33898962
The BET inhibitor attenuates the inflammatory response and cell migration in human microglial HMC3 cell line. PMID:33893325
VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics. PMID:33893273
New Insights Into Biomphalysin Gene Family Diversification in the Vector Snail Biomphalaria glabrata. PMID:33868258
Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes. PMID:33861755
The connectome of neural crest enhancers reveals regulatory features of signaling systems. PMID:33852891
Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit. PMID:33846596
A Positive Feedback Loop of Long Noncoding RNA LINC00152 and KLF5 Facilitates Breast Cancer Growth. PMID:33842324
CDX2 regulates interleukin-33 gene expression in intestinal epithelial cells (LS174T). PMID:33838073
DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch Telencephalon. PMID:33816458
Sublytic C5b-9 induces glomerular mesangial cell proliferation via ERK1/2-dependent SOX9 phosphorylation and acetylation by enhancing Cyclin D1 in rat Thy-1 nephritis. PMID:33811247
Energy stress-induced linc01564 activates the serine synthesis pathway and facilitates hepatocellular carcinogenesis. PMID:33742121
A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells. PMID:33712417
Changes in both trans- and cis-regulatory elements mediate insecticide resistance in a lepidopteron pest, Spodoptera exigua. PMID:33690635
Loop competition and extrusion model predicts CTCF interaction specificity. PMID:33594051
Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging. PMID:33571444
Early growth response 2 (EGR2) is a novel regulator of the senescence programme. PMID:33547862
Molecular characterization of atherosclerosis in HIV positive persons. PMID:33547350
Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development. PMID:33544077
Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. PMID:33539344
Human MiniPromoters for ocular-rAAV expression in ON bipolar, cone, corneal, endothelial, Müller glial, and PAX6 cells. PMID:33531684
The transcription factor PBX3 promotes tumor cell growth through transcriptional suppression of the tumor suppressor p53. PMID:33526870
Computational biology: deep learning. PMID:33525807
Systematic analysis of binding of transcription factors to noncoding variants. PMID:33505025
Regulation of Bcl-XL by non-canonical NF-κB in the context of CD40-induced drug resistance in CLL. PMID:33495554
Polymorphism rs368234815 of interferon lambda 4 gene and spontaneous clearance of hepatitis C virus in haemodialysis patients: a case-control study. PMID:33482747
A regulatory sub-circuit downstream of Wnt signaling controls developmental transitions in neural crest formation. PMID:33465092
A computational framework for identifying the transcription factors involved in enhancer-promoter loop formation. PMID:33425492
Landscape and Dynamics of the Transcriptional Regulatory Network During Natural Killer Cell Differentiation. PMID:33385611
Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo. PMID:33290745
TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains. PMID:33273453
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. PMID:33268350
Multi-Omics Identifies Circulating miRNA and Protein Biomarkers for Facioscapulohumeral Dystrophy. PMID:33228131
STAT4 targets KISS1 to promote the apoptosis of ovarian granulosa cells. PMID:33218349
Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis. PMID:33203843
Inward Rectifier K+ Currents Contribute to the Proarrhythmic Electrical Phenotype of Atria Overexpressing Cyclic Adenosine Monophosphate Response Element Modulator Isoform CREM-IbΔC-X. PMID:33191843
Smarcd1 Inhibits the Malignant Phenotypes of Human Glioblastoma Cells via Crosstalk with Notch1. PMID:33190170
A circular RNA generated from an intron of the insulin gene controls insulin secretion. PMID:33154349
Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome. PMID:33092533
TET1 Interacts Directly with NANOG via Independent Domains Containing Hydrophobic and Aromatic Residues. PMID:33058869
Differential abilities to engage inaccessible chromatin diversify vertebrate Hox binding patterns. PMID:33028607
Heat stress-induced HSP90 expression is dependent on ERK and HSF1 activation in turbot (Scophthalmus maximus) kidney cells. PMID:33025381
Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D. PMID:32999275
Tissue-specific usage of transposable element-derived promoters in mouse development. PMID:32988383
Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma. PMID:32974985
hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets. PMID:32858223
MNX1 Promotes Malignant Progression of Cervical Cancer via Repressing the Transcription of p21cip1. PMID:32850410
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans' Gene Expression Data. PMID:32759329
Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout. PMID:32738045
Occupancy maps of 208 chromatin-associated proteins in one human cell type. PMID:32728244
IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis. PMID:32679107
Genetic variability, phylogeny and functional implication of the long control region in human papillomavirus type 16, 18 and 58 in Chengdu, China. PMID:32677948
Inherited variant in NFκB-1 promoter is associated with increased risk of IBD in an Algerian population and modulates SOX9 binding. PMID:32671985
Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers That Drive Differentiation of Pancreatic Cells. PMID:32655276
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation. PMID:32637041
Phenotypic Analysis of Mutants of Ergosterol Biosynthesis Genes (ERG3 and ERG4) in the Red Yeast Xanthophyllomyces dendrorhous. PMID:32612595
Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting. PMID:32574217
Rapid and Efficient Synthetic Assembly of Multiplex Luciferase Reporter Plasmids for the Simultaneous Monitoring of Up to Six Cellular Signaling Pathways. PMID:32539183
A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. PMID:32483364
A transcriptome-based approach to identify functional modules within and across primary human immune cells. PMID:32469933
Recent development of AAV-based gene therapies for inner ear disorders. PMID:32424232
Tropomyosin 1 genetically constrains in vitro hematopoiesis. PMID:32408895
Genomic competition for noise reduction shaped evolutionary landscape of mir-4673. PMID:32376854
The SP1-12LOX axis promotes chemoresistance and metastasis of ovarian cancer. PMID:32375633
Sex chromosome evolution in parasitic nematodes of humans. PMID:32327641
RUNX2 co-operates with EGR1 to regulate osteogenic differentiation through Htra1 enhancers. PMID:32324256
LPPR4 promotes peritoneal metastasis via Sp1/integrin α/FAK signaling in gastric cancer. PMID:32266108
Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk. PMID:32220312
Runt-related transcription factor 1 promotes apoptosis and inhibits neuroblastoma progression in vitro and in vivo. PMID:32197643
ZBP1 (DAI/DLM-1) promotes osteogenic differentiation while inhibiting adipogenic differentiation in mesenchymal stem cells through a positive feedback loop of Wnt/β-catenin signaling. PMID:32195010
Tbx2a Modulates Switching of RH2 and LWS Opsin Gene Expression. PMID:32191319
BLAMM: BLAS-based algorithm for finding position weight matrix occurrences in DNA sequences on CPUs and GPUs. PMID:32164557
The Dm-Myb Oncoprotein Contributes to Insulator Function and Stabilizes Repressive H3K27me3 PcG Domains. PMID:32160531
Multi-kinase control of environmental stress responsive transcription. PMID:32160258
Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules. PMID:32153638
Estrogen Receptor, Inflammatory, and FOXO Transcription Factors Regulate Expression of Myasthenia Gravis-Associated Circulating microRNAs. PMID:32153563
WDR63 inhibits Arp2/3-dependent actin polymerization and mediates the function of p53 in suppressing metastasis. PMID:32128961
Epigenetic silencing of heat shock protein 70 through DNA hypermethylation in pseudoexfoliation syndrome and glaucoma. PMID:32127624
The Coup-TFII orphan nuclear receptor is an activator of the γ-globin gene. PMID:32107331
Splicing of enhancer-associated lincRNAs contributes to enhancer activity. PMID:32086317
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. PMID:32084333
Sex differences in spiders: from phenotype to genomics. PMID:32052129
Regenerative lineages and immune-mediated pruning in lung cancer metastasis. PMID:32042191
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. PMID:32033573
Candidate SNP Markers of Atherogenesis Significantly Shifting the Affinity of TATA-Binding Protein for Human Gene Promoters show stabilizing Natural Selection as a Sum of Neutral Drift Accelerating Atherogenesis and Directional Natural Selection Slowing It. PMID:32033288
A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. PMID:31995498
A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV. PMID:31968263
Components from the Human c-myb Transcriptional Regulation System Reactivate Epigenetically Repressed Transgenes. PMID:31947658
The endoplasmic reticulum acetyltransferases ATase1/NAT8B and ATase2/NAT8 are differentially regulated to adjust engagement of the secretory pathway. PMID:31945187
Estrogen-induced FOS-like 1 regulates matrix metalloproteinase expression and the motility of human endometrial and decidual stromal cells. PMID:31937587
Purβ promotes hepatic glucose production by increasing Adcy6 transcription. PMID:31918924
Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes. PMID:31911677
A gene regulatory network controls the balance between mesendoderm and ectoderm at pluripotency exit. PMID:31885203
Multi-species annotation of transcriptome and chromatin structure in domesticated animals. PMID:31884969
Representation learning of genomic sequence motifs with convolutional neural networks. PMID:31856220
Multivariable regulation of gene expression plasticity in metazoans. PMID:31795914
Multiple selective sweeps of ancient polymorphisms in and around LTα located in the MHC class III region on chromosome 6. PMID:31791241
A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits. PMID:31744902
Assessment of computational methods for the analysis of single-cell ATAC-seq data. PMID:31739806
JASPAR 2020: update of the open-access database of transcription factor binding profiles. PMID:31701148
Enhanced transgene expression using two β-globin MARs flanking expression cassettes in stably transfected CHO-K1 cells. PMID:31696040
Reprogramming of DNA methylation at NEUROD2-bound sequences during cortical neuron differentiation. PMID:31681843
NF-κB-Dependent IFIT3 Induction by HBx Promotes Hepatitis B Virus Replication. PMID:31681236
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs. PMID:31653198
A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs. PMID:31603892
Annotations capturing cell type-specific TF binding explain a large fraction of disease heritability. PMID:31595288
EnContact: predicting enhancer-enhancer contacts using sequence-based deep learning model. PMID:31565573
Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration. PMID:31560769
Deconvolution of transcriptional networks identifies TCF4 as a master regulator in schizophrenia. PMID:31535015
Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. PMID:31533632
Bioinformatics Discovery of Putative Enhancers within Mouse Odorant Receptor Gene Clusters. PMID:31529021
The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment. PMID:31507631
Genome-wide effects of social status on DNA methylation in the brain of a cichlid fish, Astatotilapia burtoni. PMID:31506062
CiiiDER: A tool for predicting and analysing transcription factor binding sites. PMID:31483836
YAP1 subgroup supratentorial ependymoma requires TEAD and nuclear factor I-mediated transcriptional programmes for tumorigenesis. PMID:31477715
Interaction of Genetic Variations in NFE2L2 and SELENOS Modulates the Risk of Hashimoto's Thyroiditis. PMID:31426718
Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human. PMID:31400206
Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data. PMID:31345953
Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network. PMID:31336830
A step-by-step guide to analyzing CAGE data using R/Bioconductor. PMID:31327999
Conservation, acquisition, and functional impact of sex-biased gene expression in mammals. PMID:31320509
Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development. PMID:31302154
NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region. PMID:31296853
Transcriptome analysis reveals candidate genes related to phosphorus starvation tolerance in sorghum. PMID:31296169
Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming. PMID:31271750
Long noncoding RNA EMS connects c-Myc to cell cycle control and tumorigenesis. PMID:31262817
Efflux pumps as an additional source of resistance to trichothecenes in Fusarium proliferatum and Fusarium oxysporum isolates. PMID:31250288
HNF4α and CDX2 Regulate Intestinal YAP1 Promoter Activity. PMID:31216773
Human papillomavirus 16E6/E7 activates autophagy via Atg9B and LAMP1 in cervical cancer cells. PMID:31215164
Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits. PMID:31186305
Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster. PMID:31175824
MTTFsite: cross-cell type TF binding site prediction by using multi-task learning. PMID:31161194
A common variant of RIP3 promoter region is associated with poor prognosis in heart failure patients by influencing SOX17 binding. PMID:31148336
Impact of cancer mutational signatures on transcription factor motifs in the human genome. PMID:31109337
MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites. PMID:31074373
ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery. PMID:31070745
De novo emergence and potential function of human-specific tandem repeats in brain-related loci. PMID:31069507
Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. PMID:31061989
Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin. PMID:31044167
FeatSNP: An Interactive Database for Brain-Specific Epigenetic Annotation of Human SNPs. PMID:31001319
Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors. PMID:30996347
The Stat3-Fam3a axis promotes muscle stem cell myogenic lineage progression by inducing mitochondrial respiration. PMID:30996264
Analysis of the role of mutations in the KMT2D histone lysine methyltransferase in bladder cancer. PMID:30984543
Sterol Regulatory Element-Binding Protein (Sre1) Promotes the Synthesis of Carotenoids and Sterols in Xanthophyllomyces dendrorhous. PMID:30984134
Reproducible big data science: A case study in continuous FAIRness. PMID:30973881
Intergenerational epigenetic inheritance of cancer susceptibility in mammals. PMID:30963999
DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. PMID:30948436
Forkhead box O1 (FOXO1) controls the migratory response of Toll-like receptor (TLR3)-stimulated human mesenchymal stromal cells. PMID:30944148
Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Regulatory Regions of Primate Brain-Related Genes. PMID:30930929
FactorNet: A deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data. PMID:30922998
DNA-protein interaction: identification, prediction and data analysis. PMID:30915687
SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing. PMID:30903136
Altered Promoter and G-Box Binding Factor for 1-Deoxy-d-Xylulose-5-Phosphate Synthase Gene Grown from Poa pratensis Seeds after Spaceflight. PMID:30901811
Activation of naïve CD4+ T cells re-tunes STAT1 signaling to deliver unique cytokine responses in memory CD4+ T cells. PMID:30890796
Whole genome sequencing data and analyses of the underlying SUP35 transcriptional regulation for a Saccharomyces cerevisiae nonsense suppressor mutant. PMID:30788402
Probing transcription factor combinatorics in different promoter classes and in enhancers. PMID:30709337
Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells. PMID:30697231
The Transcription Factor Function of Parkin: Breaking the Dogma. PMID:30697141
Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. PMID:30696717
Venous identity requires BMP signalling through ALK3. PMID:30692543
Disrupting the IL-36 and IL-23/IL-17 loop underlies the efficacy of calcipotriol and corticosteroid therapy for psoriasis. PMID:30674716
Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes. PMID:30673601
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution. PMID:30664627
Expression Changes of Structural Protein Genes May Be Related to Adaptive Skin Characteristics Specific to Humans. PMID:30657921
Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. PMID:30643296
Unique Transcriptional Architecture in Airway Epithelial Cells and Macrophages Shapes Distinct Responses following Influenza Virus Infection Ex Vivo. PMID:30626665
lncRNA SNHG6 regulates EZH2 expression by sponging miR-26a/b and miR-214 in colorectal cancer. PMID:30626446
Constructing tissue-specific transcriptional regulatory networks via a Markov random field. PMID:30598101
Functional characterization of the ZEB2 regulatory landscape. PMID:30590588
Human genome-wide measurement of drug-responsive regulatory activity. PMID:30575722
Performance evaluation for MOTIFSIM. PMID:30574025
Comparative transcriptomic analysis of bovine papillomatosis. PMID:30567500
Comprehensive profiling of the fission yeast transcription start site activity during stress and media response. PMID:30566651
The genomic landscape of molecular responses to natural drought stress in Panicum hallii. PMID:30523281
Control of neural crest multipotency by Wnt signaling and the Lin28/let-7 axis. PMID:30520734
p73 regulates ependymal planar cell polarity by modulating actin and microtubule cytoskeleton. PMID:30518789
Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica. PMID:30518677
Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in Drosophila and beyond. PMID:30469390
The protective microRNA-199a-5p-mediated unfolded protein response in hypoxic cardiomyocytes is regulated by STAT3 pathway. PMID:30426460
A cancer tissue-specific FAM72 expression profile defines a novel glioblastoma multiform (GBM) gene-mutation signature. PMID:30414097
ENHO, RXRA, and LXRA polymorphisms and dyslipidaemia, related comorbidities and survival in haemodialysis patients. PMID:30413149
Evolution and functional characterization of pectate lyase PEL12, a member of a highly expanded Clonostachys rosea polysaccharide lyase 1 family. PMID:30404596
Unbalanced YAP-SOX9 circuit drives stemness and malignant progression in esophageal squamous cell carcinoma. PMID:30401982
Human retinoic acid-regulated CD161+ regulatory T cells support wound repair in intestinal mucosa. PMID:30397350
Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure. PMID:30375404
Unraveling the transcriptional regulation of TWIST1 in limb development. PMID:30372441
Gene expression variability across cells and species shapes innate immunity. PMID:30356220
Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation. PMID:30355343
Long non-coding RNA-dependent mechanism to regulate heme biosynthesis and erythrocyte development. PMID:30349036
Aberrant PRDM9 expression impacts the pan-cancer genomic landscape. PMID:30341163
MODSIDE: a motif discovery pipeline and similarity detector. PMID:30340511
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features. PMID:30310060
TEPIC 2-an extended framework for transcription factor binding prediction and integrative epigenomic analysis. PMID:30304373
Dataset on the response of Hut78 cells to novel rexinoids. PMID:30294626
Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape. PMID:30279501
TFAP2 transcription factors are regulators of lipid droplet biogenesis. PMID:30256193
An Ancient Fecundability-Associated Polymorphism Creates a GATA2 Binding Site in a Distal Enhancer of HLA-F. PMID:30245028
ΔNp63α Suppresses TGFB2 Expression and RHOA Activity to Drive Cell Proliferation in Squamous Cell Carcinomas. PMID:30232004
Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease. PMID:30224808
Zebrafish blastomere screen identifies retinoic acid suppression of MYB in adenoid cystic carcinoma. PMID:30209067
Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation. PMID:30199532
Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid. PMID:30154523
Identification of TRIM14 as a Type I IFN-Stimulated Gene Controlling Hepatitis B Virus Replication by Targeting HBx. PMID:30150992
Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression. PMID:30146478
Promoters of Arabidopsis Casein kinase I-like 2 and 7 confer specific high-temperature response in anther. PMID:30145767
Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. PMID:30139913
Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster. PMID:30111890
Gene regulatory network construction identified NFYA as a diffuse subtype-specific prognostic factor in gastric cancer. PMID:30106137
Disentangling transcription factor binding site complexity. PMID:30085218
On the problem of confounders in modeling gene expression. PMID:30084962
FACT Sets a Barrier for Cell Fate Reprogramming in Caenorhabditis elegans and Human Cells. PMID:30078731
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. PMID:30078726
Spatial regulation of expanded transcription in the Drosophila wing imaginal disc. PMID:30063727
The Role of m6A/m-RNA Methylation in Stress Response Regulation. PMID:30048615
Age- and quality-dependent DNA methylation correlate with melanin-based coloration in a wild bird. PMID:30038756
Pax-5 Inhibits NF-κB Activity in Breast Cancer Cells Through IKKε and miRNA-155 Effectors. PMID:30032344
Chromatin Loop Formation Induced by a Subtelomeric Protosilencer Represses EPA Genes in Candida glabrata. PMID:30002080
Pharmacogenomics of Vincristine-Induced Peripheral Neuropathy Implicates Pharmacokinetic and Inherited Neuropathy Genes. PMID:29999516
Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells. PMID:29981477
Gene Regulatory Variation in Drosophila melanogaster Renal Tissue. PMID:29976765
The VTI1A-TCF4 colon cancer fusion protein is a dominant negative regulator of Wnt signaling and is transcriptionally regulated by intestinal homeodomain factor CDX2. PMID:29975781
Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development. PMID:29972771
Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. PMID:29958539
Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits. PMID:29945546
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. PMID:29936186
C/EBPβ Promotes STAT3 Expression and Affects Cell Apoptosis and Proliferation in Porcine Ovarian Granulosa Cells. PMID:29899261
Modeling circadian variability of core-clock and clock-controlled genes in four tissues of the rat. PMID:29894471
MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements. PMID:29893919
The role of Twist1 in mutant huntingtin-induced transcriptional alterations and neurotoxicity. PMID:29891550
DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data. PMID:29890948
Muscle miRNAome shows suppression of chronic inflammatory miRNAs with both prednisone and vamorolone. PMID:29883261
Interleukin-like EMT inducer (ILEI) promotes melanoma invasiveness and is transcriptionally up-regulated by upstream stimulatory factor-1 (USF-1). PMID:29871931
Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response. PMID:29871881
Landscape of transcriptional deregulation in lung cancer. PMID:29866045
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods. PMID:29855387
Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files. PMID:29850891
Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. PMID:29844026
Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS. PMID:29797095
Carbonic anhydrase related protein expression in astrocytomas and oligodendroglial tumors. PMID:29792187
Molecular and Functional Sex Differences of Noradrenergic Neurons in the Mouse Locus Coeruleus. PMID:29791834
The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia. PMID:29785028
Cloning and Transcriptional Activity Analysis of the Porcine Abcb1 Gene Promoter: Transcription Factor Sp1 Regulates the Expression of Porcine Abcb1. PMID:29780320
Identification of Novel Functional Variants of SIN3A and SRSF1 among Somatic Variants in Acute Myeloid Leukemia Patients. PMID:29764005
Diverse reprogramming codes for neuronal identity. PMID:29743677
NFE2-Related Transcription Factor 2 Coordinates Antioxidant Defense with Thyroglobulin Production and Iodination in the Thyroid Gland. PMID:29742982
REGGAE: a novel approach for the identification of key transcriptional regulators. PMID:29741575
Towards a map of cis-regulatory sequences in the human genome. PMID:29733395
Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris. PMID:29728068
An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation. PMID:29706346
A novel gene expression analytics-based approach to structure aided design of rexinoids for development as next-generation cancer therapeutics. PMID:29704526
The polymorphisms of LCR, E6, and E7 of HPV-58 isolates in Yunnan, Southwest China. PMID:29695285
Transcript-indexed ATAC-seq for precision immune profiling. PMID:29686426
Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation. PMID:29674676
Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers. PMID:29670109
Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. PMID:29659982
Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs). PMID:29659815
Interactions between genetic variation and cellular environment in skeletal muscle gene expression. PMID:29659628
FAR2 is associated with kidney disease in mice and humans. PMID:29652635
Emerging applications of genome-editing technology to examine functionality of GWAS-associated variants for complex traits. PMID:29652634
Ldb1- and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in the retina. PMID:29650591
Neonatal Genistein Exposure and Glucocorticoid Signaling in the Adult Mouse Uterus. PMID:29624291
Identification and functional analysis of glycemic trait loci in the China Health and Nutrition Survey. PMID:29621232
Global dynamics of stage-specific transcription factor binding during thymocyte development. PMID:29618724
Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. PMID:29618487
DeFine: deep convolutional neural networks accurately quantify intensities of transcription factor-DNA binding and facilitate evaluation of functional non-coding variants. PMID:29617928
A novel method for improved accuracy of transcription factor binding site prediction. PMID:29617876
Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity. PMID:29617378
Comparative Serum Challenges Show Divergent Patterns of Gene Expression and Open Chromatin in Human and Chimpanzee. PMID:29608722
Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding. PMID:29605182
SP8 Transcriptional Regulation of Cyclin D1 During Mouse Early Corticogenesis. PMID:29599703
UBE2C Is a Transcriptional Target of the Cell Cycle Regulator FOXM1. PMID:29596365
An intronic VNTR affects splicing of ABCA7 and increases risk of Alzheimer's disease. PMID:29589097
Sequential regulatory activity prediction across chromosomes with convolutional neural networks. PMID:29588361
Integrating ChIP-seq with other functional genomics data. PMID:29579165
Linkage disequilibrium and functional analysis of PRE1 insertion together with SNPs in the promoter region of IGFBP7 gene in different pig breeds. PMID:29574509
Tetramerization of MADS family transcription factors SEPALLATA3 and AGAMOUS is required for floral meristem determinacy in Arabidopsis. PMID:29562355
De novo mutations in regulatory elements in neurodevelopmental disorders. PMID:29562236
System analysis of the regulation of the immune response by CD147 and FOXC1 in cancer cell lines. PMID:29560120
Expression of Carbonic Anhydrase III, a Nucleus Pulposus Phenotypic Marker, is Hypoxia-responsive and Confers Protection from Oxidative Stress-induced Cell Death. PMID:29559661
BRD7 expression and c-Myc activation forms a double-negative feedback loop that controls the cell proliferation and tumor growth of nasopharyngeal carcinoma by targeting oncogenic miR-141. PMID:29559001
Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution. PMID:29544533
Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci. PMID:29540241
esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis. PMID:29522192
Characterization of the human RFX transcription factor family by regulatory and target gene analysis. PMID:29510665
From gene networks to drugs: systems pharmacology approaches for AUD. PMID:29497781
Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. PMID:29491135
NRF2 regulates core and stabilizing circadian clock loops, coupling redox and timekeeping in Mus musculus. PMID:29481323
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. PMID:29434377
MAGE-A11 is activated through TFCP2/ZEB1 binding sites de-methylation as well as histone modification and facilitates ESCC tumor growth. PMID:29423052
Treatment-associated TP53 DNA-binding domain missense mutations in the pathogenesis of secondary gliosarcoma. PMID:29416795
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding. PMID:29409522
Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets. PMID:29385521
DNA-binding landscape of IRF3, IRF5 and IRF7 dimers: implications for dimer-specific gene regulation. PMID:29361124
Multiplatform next-generation sequencing identifies novel RNA molecules and transcript isoforms of the endogenous retrovirus isolated from cultured cells. PMID:29361122
RGBM: regularized gradient boosting machines for identification of the transcriptional regulators of discrete glioma subtypes. PMID:29361062
Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements. PMID:29360936
FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch. PMID:29360038
Sox2 is required for olfactory pit formation and olfactory neurogenesis through BMP restriction and Hes5 upregulation. PMID:29352015
Integrative Genomic Analysis Predicts Causative Cis-Regulatory Mechanisms of the Breast Cancer-Associated Genetic Variant rs4415084. PMID:29351903
The Jun/miR-22/HuR regulatory axis contributes to tumourigenesis in colorectal cancer. PMID:29351796
INO80 Chromatin Remodeling Coordinates Metabolic Homeostasis with Cell Division. PMID:29346761
Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis. PMID:29342503
Relationship between histone modifications and transcription factor binding is protein family specific. PMID:29326300
Functional characterization of adaptive variation within a cis-regulatory element influencing Drosophila melanogaster growth. PMID:29324742
The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis. PMID:29307494
Local sequence features that influence AP-1 cis-regulatory activity. PMID:29305491
Transcription Factor and lncRNA Regulatory Networks Identify Key Elements in Lung Adenocarcinoma. PMID:29303984
Global mapping of transcription factor motifs in human aging. PMID:29293662
Probing instructions for expression regulation in gene nucleotide compositions. PMID:29293496
METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m6A Modification. PMID:29290617
Long-Range Signaling Activation and Local Inhibition Separate the Mesoderm and Endoderm Lineages. PMID:29275993
Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis. PMID:29273624
AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection. PMID:29272704
TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. PMID:29272447
THiCweed: fast, sensitive detection of sequence features by clustering big datasets. PMID:29267972
Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10-clade. PMID:29258424
Novel schizophrenia risk factor pathways regulate FEZ1 to advance oligodendroglia development. PMID:29249816
Central role of the p53 pathway in the noncoding-RNA response to oxidative stress. PMID:29242407
FoxO1 is a regulator of MHC-II expression and anti-tumor effect of tumor-associated macrophages. PMID:29238041
EGFR feedback-inhibition by Ran-binding protein 6 is disrupted in cancer. PMID:29229958
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. PMID:29227469
Kiwifruit SVP2 controls developmental and drought-stress pathways. PMID:29222611
RetrogeneDB-a database of plant and animal retrocopies. PMID:29220443
Predicting enhancers with deep convolutional neural networks. PMID:29219068
Scoring Targets of Transcription in Bacteria Rather than Focusing on Individual Binding Sites. PMID:29213263
Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle. PMID:29212449
LAST, a c-Myc-inducible long noncoding RNA, cooperates with CNBP to promote CCND1 mRNA stability in human cells. PMID:29199958
SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site. PMID:29196557
Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer's disease resilience. PMID:29183403
A hypermorphic antioxidant response element is associated with increased MS4A6A expression and Alzheimer's disease. PMID:29179108
CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors. PMID:29178828
HOXC13 promotes proliferation of esophageal squamous cell carcinoma via repressing transcription of CASP3. PMID:29168599
Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials. PMID:29167532
NDUFA4L2 is associated with clear cell renal cell carcinoma malignancy and is regulated by ELK1. PMID:29158991
Association of melatonin membrane receptor 1A/1B gene polymorphisms with the occurrence and metastasis of hepatocellular carcinoma. PMID:29156748
Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins. PMID:29146583
Nucleotide patterns aiding in prediction of eukaryotic promoters. PMID:29141011
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. PMID:29140473
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. PMID:29140464
Mice Lacking EGR1 Have Impaired Clock Gene (BMAL1) Oscillation, Locomotor Activity, and Body Temperature. PMID:29138967
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. PMID:29126285
Comprehensive bioinformatics analysis of the characterization and determination underlying mechanisms of over-expression and co-expression of genes residing on 20q in colorectal cancer. PMID:29108255
Deconvolution of Transcriptional Networks in Post-Traumatic Stress Disorder Uncovers Master Regulators Driving Innate Immune System Function. PMID:29101382
Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea. PMID:29100657
Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system. PMID:29087374
Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis. PMID:29074988
OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes. PMID:29069459
Chromatin accessibility prediction via a hybrid deep convolutional neural network. PMID:29069282
Cis-regulatory landscapes of four cell types of the retina. PMID:29059322
Common microRNA-mRNA interactions exist among distinct porcine iPSC lines independent of their metastable pluripotent states. PMID:29048434
Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone. PMID:29036586
cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches. PMID:29036576
NEUROG1 Regulates CDK2 to Promote Proliferation in Otic Progenitors. PMID:29033307
Loci associated with skin pigmentation identified in African populations. PMID:29025994
Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. PMID:29025895
SHH signaling directed by two oral epithelium-specific enhancers controls tooth and oral development. PMID:29021530
Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity. PMID:28985297
Logo2PWM: a tool to convert sequence logo to position weight matrix. PMID:28984206
SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome. PMID:28968739
Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints. PMID:28961735
Identification of breast cancer associated variants that modulate transcription factor binding. PMID:28957321
Bicarbonate Recycling by HIF-1-Dependent Carbonic Anhydrase Isoforms 9 and 12 Is Critical in Maintaining Intracellular pH and Viability of Nucleus Pulposus Cells. PMID:28940640
Pioneer Factors FOXA1 and FOXA2 Assist Selective Glucocorticoid Receptor Signaling in Human Endometrial Cells. PMID:28938408
Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation. PMID:28931413
Identification of fasciclin-like arabinogalactan proteins in textile hemp (Cannabis sativa L.): in silico analyses and gene expression patterns in different tissues. PMID:28931375
Predicting Variation of DNA Shape Preferences in Protein-DNA Interaction in Cancer Cells with a New Biophysical Model. PMID:28927002
SOX14 activates the p53 signaling pathway and induces apoptosis in a cervical carcinoma cell line. PMID:28926586
Exploiting Drug Addiction Mechanisms to Select against MAPKi-Resistant Melanoma. PMID:28923912
Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments. PMID:28911122
Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints. PMID:28904015
Tumor necrosis factor‑α and interleukin‑6 suppress microRNA‑1275 transcription in human adipocytes through nuclear factor‑κB. PMID:28901460
Insm1a Regulates Motor Neuron Development in Zebrafish. PMID:28894416
An embryonic system to assess direct and indirect Wnt transcriptional targets. PMID:28894169
A functional genomics predictive network model identifies regulators of inflammatory bowel disease. PMID:28892060
Type 1 Interferons Potentiate Human CD8+ T-Cell Cytotoxicity Through a STAT4- and Granzyme B-Dependent Pathway. PMID:28877912
An Alternative STAT Signaling Pathway Acts in Viral Immunity in Caenorhabditis elegans. PMID:28874466
The transcription factor Maf-S regulates metabolic resistance to insecticides in the malaria vector Anopheles gambiae. PMID:28854876
Combinatorial regulation of a Blimp1 (Prdm1) enhancer in the mouse retina. PMID:28829770
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. PMID:28825706
Association between Promoter Methylation of Gene ERCC3 and Benzene Hematotoxicity. PMID:28813025
Ethanol Exposure Regulates Gabra1 Expression via Histone Deacetylation at the Promoter in Cultured Cortical Neurons. PMID:28798030
Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs. PMID:28786034
Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues. PMID:28783152
Genetic variability and functional implication of the long control region in HPV-16 variants in Southwest China. PMID:28767682
Induction of alpha-methylacyl-CoA racemase by miR-138 via up-regulation of β-catenin in prostate cancer cells. PMID:28741117
Characterization of the cytochrome P450 monooxygenase genes (P450ome) from the carotenogenic yeast Xanthophyllomyces dendrorhous. PMID:28724407
Up-regulation of CDK16 by multiple mechanisms in hepatocellular carcinoma promotes tumor progression. PMID:28716136
An efficient algorithm for improving structure-based prediction of transcription factor binding sites. PMID:28715997
An erythroid-specific ATP2B4 enhancer mediates red blood cell hydration and malaria susceptibility. PMID:28714864
Activating transcription factor 3 promotes loss of the acinar cell phenotype in response to cerulein-induced pancreatitis in mice. PMID:28701342
Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses. PMID:28700586
Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. PMID:28691125
Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1. PMID:28676792
Inherited determinants of early recurrent somatic mutations in prostate cancer. PMID:28663546
LASSIM-A network inference toolbox for genome-wide mechanistic modeling. PMID:28640810
The LDB1 Complex Co-opts CTCF for Erythroid Lineage-Specific Long-Range Enhancer Interactions. PMID:28636938
MOTIFSIM 2.1: An Enhanced Software Platform for Detecting Similarity in Multiple DNA Motif Data Sets. PMID:28632401
Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors. PMID:28625481
Single-cell profiling reveals heterogeneity and functional patterning of GPCR expression in the vascular system. PMID:28621310
A hormonal cue promotes timely follicle cell migration by modulating transcription profiles. PMID:28610887
Dynamic maps of UV damage formation and repair for the human genome. PMID:28607063
RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. PMID:28591841
High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor. PMID:28588247
Challenges and progress in interpretation of non-coding genetic variants associated with human disease. PMID:28581336
UROPA: a tool for Universal RObust Peak Annotation. PMID:28572580
Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa). PMID:28560587
Transversions have larger regulatory effects than transitions. PMID:28525990
Role of transgelin-2 in diabetes-associated pancreatic ductal adenocarcinoma. PMID:28521289
NMI inhibits cancer stem cell traits by downregulating hTERT in breast cancer. PMID:28492540
RegulatorTrail: a web service for the identification of key transcriptional regulators. PMID:28472408
Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes. PMID:28467369
Orphan CpG islands define a novel class of highly active enhancers. PMID:28448736
Oncogenic effects of evolutionarily conserved noncoding RNA ECONEXIN on gliomagenesis. PMID:28368417
NFAT5 and SLC4A10 Loci Associate with Plasma Osmolality. PMID:28360221
Transcription factor-DNA binding: beyond binding site motifs. PMID:28359978
Significance evaluation in factor graphs. PMID:28359297
ML2Motif-Reliable extraction of discriminative sequence motifs from learning machines. PMID:28346487
Identification and comparative analysis of the epidermal differentiation complex in snakes. PMID:28345630
Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility. PMID:28334916
The microRNA-302b-inhibited insulin-like growth factor-binding protein 2 signaling pathway induces glioma cell apoptosis by targeting nuclear factor IA. PMID:28323865
DNA methylation patterns of behavior-related gene promoter regions dissect the gray wolf from domestic dog breeds. PMID:28321510
Recessive coding and regulatory mutations in FBLIM1 underlie the pathogenesis of chronic recurrent multifocal osteomyelitis (CRMO). PMID:28301468
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation. PMID:28288100
Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting. PMID:28287101
Down-regulation of Forkhead box protein A1 (FOXA1) leads to cancer stem cell-like properties in tamoxifen-resistant breast cancer cells through induction of interleukin-6. PMID:28270510
Notch1-promoted TRPA1 expression in erythroleukemic cells suppresses erythroid but enhances megakaryocyte differentiation. PMID:28220825
Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo. PMID:28174238
Genome-wide association of white blood cell counts in Hispanic/Latino Americans: the Hispanic Community Health Study/Study of Latinos. PMID:28158719
Prediction of bipartite transcriptional regulatory elements using transcriptome data of Arabidopsis. PMID:28158431
LincRNA-Gm4419 knockdown ameliorates NF-κB/NLRP3 inflammasome-mediated inflammation in diabetic nephropathy. PMID:28151474
Enhancing gene regulatory network inference through data integration with markov random fields. PMID:28145456
Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex. PMID:28112643
Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF. PMID:28103242
Bdf1 Bromodomains Are Essential for Meiosis and the Expression of Meiotic-Specific Genes. PMID:28068333
TBX5: A Key Regulator of Heart Development. PMID:28057264
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans. PMID:28036392
Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms. PMID:28031487
Network Analysis-Based Approach for Exploring the Potential Diagnostic Biomarkers of Acute Myocardial Infarction. PMID:28018242
A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development. PMID:28011632
Alterations in the neuropeptide galanin system in major depressive disorder involve levels of transcripts, methylation, and peptide. PMID:27940914
Genome-wide uniformity of human 'open' pre-initiation complexes. PMID:27927716
Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. PMID:27927715
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. PMID:27924042
Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation. PMID:27903902
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction. PMID:27899623
SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity. PMID:27899579
DEEP MOTIF DASHBOARD: VISUALIZING AND UNDERSTANDING GENOMIC SEQUENCES USING DEEP NEURAL NETWORKS. PMID:27896980
Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis. PMID:27881726
The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data. PMID:27863463
YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. PMID:27857184
Genetic determination of the enhanced drought resistance of rice maintainer HuHan2B by pedigree breeding. PMID:27853319
SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells. PMID:27852806
Modeling Gene Regulation in Liver Hepatocellular Carcinoma with Random Forests. PMID:27818995
An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships. PMID:27802351
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. PMID:27794045
3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes. PMID:27789693
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. PMID:27789689
Deregulation of DUX4 and ERG in acute lymphoblastic leukemia. PMID:27776115
Inhibition of Snail Family Transcriptional Repressor 2 (SNAI2) Enhances Multidrug Resistance of Hepatocellular Carcinoma Cells. PMID:27760172
Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron. PMID:27756226
An Ancient Fecundability-Associated Polymorphism Switches a Repressor into an Enhancer of Endometrial TAP2 Expression. PMID:27745831
High-resolution interrogation of functional elements in the noncoding genome. PMID:27708104
Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. PMID:27678375
WNT4 mediates estrogen receptor signaling and endocrine resistance in invasive lobular carcinoma cell lines. PMID:27650553
Identification of Novel Nuclear Factor of Activated T Cell (NFAT)-associated Proteins in T Cells. PMID:27637333
Expression dynamics, relationships, and transcriptional regulations of diverse transcripts in mouse spermatogenic cells. PMID:27560004
Decreased expression of connective tissue growth factor in non-small cell lung cancer is associated with clinicopathological variables and can be restored by epigenetic modifiers. PMID:27393180
A microRNA-328 binding site in PAX6 is associated with centrotemporal spikes of rolandic epilepsy. PMID:27386500
Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish. PMID:27356472
The genetic regulatory signature of type 2 diabetes in human skeletal muscle. PMID:27353450
Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks. PMID:27346425
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. PMID:27334471
PEDLA: predicting enhancers with a deep learning-based algorithmic framework. PMID:27329130
Parallel evolution of male germline epigenetic poising and somatic development in animals. PMID:27294618
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. PMID:27288444
Inferring RBP-Mediated Regulation in Lung Squamous Cell Carcinoma. PMID:27186987
Statistical analysis of structural determinants for protein-DNA-binding specificity. PMID:27147539
Validation of differential GDAP1 DNA methylation in alcohol dependence and its potential function as a biomarker for disease severity and therapy outcome. PMID:27128683
Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors. PMID:27124577
DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences. PMID:27084946
DNA context represents transcription regulation of the gene in mouse embryonic stem cells. PMID:27075878
System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination. PMID:27031986
Integration of Orthogonal Signaling by the Notch and Dpp Pathways in Drosophila. PMID:26975664
Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. PMID:26941778
TFBSTools: an R/bioconductor package for transcription factor binding site analysis. PMID:26794315
Regulation of c-Maf and αA-Crystallin in Ocular Lens by Fibroblast Growth Factor Signaling. PMID:26719333
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update PubMed citations: 403.

403 articles citing: JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

In Silico Analysis of CCGAC and CATGTG Cis-regulatory Elements Across Genomes Reveals their Roles in Gene Regulation under Stress. PMID:35283666
Cognate DNA Recognition by Engrailed Homeodomain Involves a Conformational Change Controlled via an Electrostatic-Spring-Loaded Latch. PMID:35269555
Potential biomarkers and signaling pathways associated with the pathogenesis of primary salivary gland carcinoma: a bioinformatics study. PMID:35012286
CREB1K292 and HINFPK330 as Putative Common Therapeutic Targets in Alzheimer's and Parkinson's Disease. PMID:34984308
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. PMID:34850907
Pharmacological Disruption of Phosphorylated Eukaryotic Initiation Factor-2α/Activating Transcription Factor 4/Indian Hedgehog Protects Intervertebral Disc Degeneration via Reducing the Reactive Oxygen Species and Apoptosis of Nucleus Pulposus Cells. PMID:34164397
ΔNp63 is a pioneer factor that binds inaccessible chromatin and elicits chromatin remodeling. PMID:33865440
What Can Machine Learning Approaches in Genomics Tell Us about the Molecular Basis of Amyotrophic Lateral Sclerosis? PMID:33256133
ROS/NF-κB Signaling Pathway-Mediated Transcriptional Activation of TRIM37 Promotes HBV-Associated Hepatic Fibrosis. PMID:32916597
Functional fine-mapping of noncoding risk variants in amyotrophic lateral sclerosis utilizing convolutional neural network. PMID:32732921
p16 deficiency attenuates intervertebral disc degeneration by adjusting oxidative stress and nucleus pulposus cell cycle. PMID:32125276
Eukaryotic transcription factors can track and control their target genes using DNA antennas. PMID:31992709
MYC and Twist1 cooperate to drive metastasis by eliciting crosstalk between cancer and innate immunity. PMID:31933479
Convolutional neural network model to predict causal risk factors that share complex regulatory features. PMID:31598692
Hamiltonian energy as an efficient approach to identify the significant key regulators in biological networks. PMID:31442253
Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network. PMID:31336830
Shiny-Seq: advanced guided transcriptome analysis. PMID:31319888
A gene regulatory network explains RET-EDNRB epistasis in Hirschsprung disease. PMID:31313802
Predicting functional variants in enhancer and promoter elements using RegulomeDB. PMID:31228310
MTTFsite: cross-cell type TF binding site prediction by using multi-task learning. PMID:31161194
HCP5 is a SMAD3-responsive long non-coding RNA that promotes lung adenocarcinoma metastasis via miR-203/SNAI axis. PMID:31131047
MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites. PMID:31074373
Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk. PMID:31064983
DNA-protein interaction: identification, prediction and data analysis. PMID:30915687
Integrated epigenomic profiling reveals endogenous retrovirus reactivation in renal cell carcinoma. PMID:30827930
Integrated Functional Genomic Analysis Enables Annotation of Kidney Genome-Wide Association Study Loci. PMID:30760496
Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation. PMID:30639098
NFAT5 up-regulates expression of the kidney-specific ubiquitin ligase gene Rnf183 under hypertonic conditions in inner-medullary collecting duct cells. PMID:30413537
Correlated Evolution of Two Copulatory Organs via a Single cis-Regulatory Nucleotide Change. PMID:30344115
Genetic determinants of childhood and adult height associated with osteosarcoma risk. PMID:30311632
Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens. PMID:30295986
Epigenetic Study in Parkinson's Disease: A Pilot Analysis of DNA Methylation in Candidate Genes in Brain. PMID:30261625
HiCDB: a sensitive and robust method for detecting contact domain boundaries. PMID:30184171
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals. PMID:30137416
YY1 binds to the E3' enhancer and inhibits the expression of the immunoglobulin κ gene via epigenetic modifications. PMID:30098214
A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease. PMID:29986096
DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP. PMID:29684008
Selection on the regulation of sympathetic nervous activity in humans and chimpanzees. PMID:29672586
A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human. PMID:29518216
The HNF1α-regulated lncRNA HNF1A-AS1 reverses the malignancy of hepatocellular carcinoma by enhancing the phosphatase activity of SHP-1. PMID:29466992
Local sequence features that influence AP-1 cis-regulatory activity. PMID:29305491
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. PMID:29140473
Ubiquitin-specific peptidase 7 (USP7)-mediated deubiquitination of the histone deacetylase SIRT7 regulates gluconeogenesis. PMID:28655758
Canonical and alternative transcript expression of PAX6 and CXCR4 in pancreatic cancer. PMID:28588695
Sox5 regulates beta-cell phenotype and is reduced in type 2 diabetes. PMID:28585545
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. PMID:28333948
A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data. PMID:28143596
Regulatory elements in molecular networks. PMID:28093886
Genome-wide identification of regulatory elements in Sertoli cells. PMID:28087634
The pan-cancer pathological regulatory landscape. PMID:28000771
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules. PMID:27871221
Methodology for single nucleotide polymorphism selection in promoter regions for clinical use. An example of its applicability. PMID:27766139
Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease. PMID:27693352
Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus. PMID:27685795
Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. PMID:27468897
Transcriptome Analysis on Monocytes from Patients with Neovascular Age-Related Macular Degeneration. PMID:27374485
PU.1 is involved in the immune response to Aspergillus fumigatus through upregulating Dectin-1 expression. PMID:27306059
Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. PMID:27297499
Apoptosis signal-regulating kinase 1 mediates the inhibitory effect of hepatocyte nuclear factor-4α on hepatocellular carcinoma. PMID:27050273
Gene regulatory mechanisms underpinning prostate cancer susceptibility. PMID:26950096
Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants. PMID:26869700
Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions. PMID:26860869
Relevance of Sp Binding Site Polymorphism in WWOX for Treatment Outcome in Pancreatic Cancer. PMID:26857392
Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. PMID:26845687
Regulation of c-Maf and αA-Crystallin in Ocular Lens by Fibroblast Growth Factor Signaling. PMID:26719333
Bioinformatic Evaluation of Transcriptional Regulation of WNT Pathway Genes with reference to Diabetic Nephropathy. PMID:26697505
Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line. PMID:26635867
The epigenomic landscape of African rainforest hunter-gatherers and farmers. PMID:26616214
The direction of cross affects [corrected] obesity after puberty in male but not female offspring. PMID:26546267
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. PMID:26531826
Transcription factor trapping by RNA in gene regulatory elements. PMID:26516199
The unique transcriptional response produced by concurrent estrogen and progesterone treatment in breast cancer cells results in upregulation of growth factor pathways and switching from a Luminal A to a Basal-like subtype. PMID:26498662
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. PMID:26424082
Mechanisms of Soybean Roots' Tolerances to Salinity Revealed by Proteomic and Phosphoproteomic Comparisons Between Two Cultivars. PMID:26407991
TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis. PMID:26394619
The transcription factor ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory. PMID:26322480
An HNF1α-regulated feedback circuit modulates hepatic fibrogenesis via the crosstalk between hepatocytes and hepatic stellate cells. PMID:26169608
A widespread role of the motif environment in transcription factor binding across diverse protein families. PMID:26160164
NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets. PMID:26146939
Identification of in vivo DNA-binding mechanisms of Pax6 and reconstruction of Pax6-dependent gene regulatory networks during forebrain and lens development. PMID:26138486
Application of Comparative Transcriptional Genomics to Identify Molecular Targets for Pediatric IBD. PMID:26085826
Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides. PMID:26016481
Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development. PMID:25990720
Cardiac gene expression data and in silico analysis provide novel insights into human and mouse taste receptor gene regulation. PMID:25986534
Gene and MicroRNA Expression Responses to Exercise; Relationship with Insulin Sensitivity. PMID:25984722
DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. PMID:25972927
Identifying TF-MiRNA Regulatory Relationships Using Multiple Features. PMID:25922940
Targeting chromatin binding regulation of constitutively active AR variants to overcome prostate cancer resistance to endocrine-based therapies. PMID:25908785
NF-κB and IRF pathways: cross-regulation on target genes promoter level. PMID:25888367
EVI1 promotes tumor growth via transcriptional repression of MS4A3. PMID:25886616
A temporal gate for viral enhancers to co-opt Toll-like-receptor transcriptional activation pathways upon acute infection. PMID:25856589
Modeling the relationship of epigenetic modifications to transcription factor binding. PMID:25820421
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. PMID:25779349
Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites. PMID:25763115
Computational methodology for ChIP-seq analysis. PMID:25741452
Gateways to the FANTOM5 promoter level mammalian expression atlas. PMID:25723102
Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells. PMID:25717144
Functional and phylogenetic characterization of proteins detected in various nematode intestinal compartments. PMID:25609831
Direct regulation of diurnal Drd3 expression and cocaine reward by NPAS2. PMID:25444159
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. PMID:25428367
Comparison of tamoxifen and letrozole response in mammary preneoplasia of ER and aromatase overexpressing mice defines an immune-associated gene signature linked to tamoxifen resistance. PMID:25421723
A sequence-specific interaction between the Saccharomyces cerevisiae rRNA gene repeats and a locus encoding an RNA polymerase I subunit affects ribosomal DNA stability. PMID:25421713
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. PMID:25411453
Conservation of trans-acting circuitry during mammalian regulatory evolution. PMID:25409825
Heat stress-induced Cup9-dependent transcriptional regulation of SIR2. PMID:25384977
DEEP: a general computational framework for predicting enhancers. PMID:25378307
Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-HTT-deficient mice. PMID:25335169
Sex steroid blockade enhances thymopoiesis by modulating Notch signaling. PMID:25332287
Kruppel-like factor-9 (KLF9) inhibits glioblastoma stemness through global transcription repression and integrin α6 inhibition. PMID:25288800
Molecular mechanism underlying the impact of vitamin D on disease activity of MS. PMID:25285313
Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. PMID:25281301
Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus. PMID:25211022
A regulatory network controls nephrocan expression and midgut patterning. PMID:25209250
Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. PMID:25198066
Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network. PMID:25163748
A bayesian framework that integrates heterogeneous data for inferring gene regulatory networks. PMID:25152886
The BCL9-2 proto-oncogene governs estrogen receptor alpha expression in breast tumorigenesis. PMID:25149534
Genistein disrupts glucocorticoid receptor signaling in human uterine endometrial Ishikawa cells. PMID:25136773
Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms. PMID:25133983
A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL. PMID:25114055
A novel MMP12 locus is associated with large artery atherosclerotic stroke using a genome-wide age-at-onset informed approach. PMID:25078452
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. PMID:25035402
Enhanced regulatory sequence prediction using gapped k-mer features. PMID:25033408
Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. PMID:25018785
Activation of hypoxia-inducible factor-1α in type 2 alveolar epithelial cell is a major driver of acute inflammation following lung contusion. PMID:25014067
The role of melanogenesis in regulation of melanoma behavior: melanogenesis leads to stimulation of HIF-1α expression and HIF-dependent attendant pathways. PMID:24997364
Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. PMID:24908250
Global view of enhancer-promoter interactome in human cells. PMID:24821768
Biased, non-equivalent gene-proximal and -distal binding motifs of orphan nuclear receptor TR4 in primary human erythroid cells. PMID:24811540
The interaction of MYC with the trithorax protein ASH2L promotes gene transcription by regulating H3K27 modification. PMID:24782528
Key regulators control distinct transcriptional programmes in blood progenitor and mast cells. PMID:24760698
STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells. PMID:24711622
Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise. PMID:24710104
Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis. PMID:24706889
Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences. PMID:24692653
Hypoxic stress facilitates acute activation and chronic downregulation of fanconi anemia proteins. PMID:24688021
Explaining the correlations among properties of mammalian promoters. PMID:24682821
Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. PMID:24680932
Coregulation of genetic programs by the transcription factors NFIB and STAT5. PMID:24678731
Evidence for local regulatory control of escape from imprinted X chromosome inactivation. PMID:24653000
TACO: a general-purpose tool for predicting cell-type-specific transcription factor dimers. PMID:24640962
Human coronary heart disease: importance of blood cellular miR-2909 RNomics. PMID:24634009
Dedifferentiation of neurons precedes tumor formation in Lola mutants. PMID:24631403
STEME: a robust, accurate motif finder for large data sets. PMID:24625410
Fuzziness and noise in nucleosomal architecture. PMID:24586063
Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data. PMID:24564528
fourSig: a method for determining chromosomal interactions in 4C-Seq data. PMID:24561615
Stem cell characteristics in glioblastoma are maintained by the ecto-nucleotidase E-NPP1. PMID:24531536
cJun promotes CNS axon growth. PMID:24521823
Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum. PMID:24516681
Viral enhancer mimicry of host innate-immune promoters. PMID:24516378
Pol II docking and pausing at growth and stress genes in C. elegans. PMID:24485661
Regulation of the dynamic chromatin architecture of the epidermal differentiation complex is mediated by a c-Jun/AP-1-modulated enhancer. PMID:24468747
Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns. PMID:24465517
Genome of the human hookworm Necator americanus. PMID:24441737
A provisional gene regulatory atlas for mouse heart development. PMID:24421884
The transcription factor T-box 3 regulates colony-stimulating factor 1-dependent Jun dimerization protein 2 expression and plays an important role in osteoclastogenesis. PMID:24394418
Basal PIR expression in HeLa cells is driven by NRF2 via evolutionary conserved antioxidant response element. PMID:24390086
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. PMID:24366875
Whole blood gene expression profiles in insulin resistant Latinos with the metabolic syndrome. PMID:24358323
Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PMID:24339764
Predicting tissue specific transcription factor binding sites. PMID:24238150
Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. PMID:24218641
Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. PMID:24205361
Fine-mapping an association of FSHR with preterm birth in a Finnish population. PMID:24205076
Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information. PMID:24204023
Putative role of HIF transcriptional activity in melanocytes and melanoma biology. PMID:24194964
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. PMID:24194598
Dynamic feedback circuits function as a switch for shaping a maturation-inducing steroid pulse in Drosophila. PMID:24173800
Discriminative motif analysis of high-throughput dataset. PMID:24162561
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. PMID:24156763
Metabolic and protein interaction sub-networks controlling the proliferation rate of cancer cells and their impact on patient survival. PMID:24154670
Associations between intronic non-B DNA structures and exon skipping. PMID:24153112
Screening for protein-DNA interactions by automatable DNA-protein interaction ELISA. PMID:24146751
Integrated module and gene-specific regulatory inference implicates upstream signaling networks. PMID:24146602
Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. PMID:24137002
Differential recruitment of coregulators to the RORA promoter adds another layer of complexity to gene (dys) regulation by sex hormones in autism. PMID:24119295
VEGFA rSNPs, transcriptional factor binding sites and human disease. PMID:24097272
Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs. PMID:24089456
Three promoters regulate the transcriptional activity of the human holocarboxylase synthetase gene. PMID:24075901
MEF2 is an in vivo immune-metabolic switch. PMID:24075010
Autoregulatory feedback controls sequential action of cis-regulatory modules at the brinker locus. PMID:24044892
A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. PMID:24006278
Identification and dissection of a key enhancer mediating cranial neural crest specific expression of transcription factor, Ets-1. PMID:23969311
A comprehensive functional portrait of two heat shock factor-type transcriptional regulators involved in Candida albicans morphogenesis and virulence. PMID:23966855
The evolution of complex gene regulation by low-specificity binding sites. PMID:23945682
Pax7 is regulated by cMyb during early neural crest development through a novel enhancer. PMID:23942518
Transcriptional network analysis for the regulation of left ventricular hypertrophy and microvascular remodeling. PMID:23929067
A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks. PMID:23917988
DNA methylation contributes to natural human variation. PMID:23908385
Computational approaches to identify functional genetic variants in cancer genomes. PMID:23900255
A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. PMID:23867016
Global gene expression analysis in human uterine epithelial cells defines new targets of glucocorticoid and estradiol antagonism. PMID:23843231
Identification of active regulatory regions from DNA methylation data. PMID:23828043
DNA methylation data analysis and its application to cancer research. PMID:23750645
Exploring the transcription factor activity in high-throughput gene expression data using RLQ analysis. PMID:23742070
Genome-wide identification of transcriptional targets of RORA reveals direct regulation of multiple genes associated with autism spectrum disorder. PMID:23697635
Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver. PMID:23682854
MEME-LaB: motif analysis in clusters. PMID:23681125
Enhancer transcripts mark active estrogen receptor binding sites. PMID:23636943
Population genomics and transcriptional consequences of regulatory motif variation in globally diverse Saccharomyces cerevisiae strains. PMID:23619145
The expression of Sox17 identifies and regulates haemogenic endothelium. PMID:23604320
Molecular cloning of doublesex genes of four cladocera (water flea) species. PMID:23575357
Under-dominance constrains the evolution of negative autoregulation in diploids. PMID:23555226
A discriminative approach for unsupervised clustering of DNA sequence motifs. PMID:23555204
VEGFA SNPs and transcriptional factor binding sites associated with high altitude sickness in Han and Tibetan Chinese at the Qinghai-Tibetan Plateau. PMID:23553563
Heritable remodeling of yeast multicellularity by an environmentally responsive prion. PMID:23540696
Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus). PMID:23532859
LASAGNA: a novel algorithm for transcription factor binding site alignment. PMID:23522376
Comparative annotation of functional regions in the human genome using epigenomic data. PMID:23482391
Regulation of SIRT1 by oxidative stress-responsive miRNAs and a systematic approach to identify its role in the endothelium. PMID:23477488
RAP: accurate and fast motif finding based on protein-binding microarray data. PMID:23464877
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. PMID:23431001
Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development. PMID:23393190
PRISM offers a comprehensive genomic approach to transcription factor function prediction. PMID:23382538
A high-resolution enhancer atlas of the developing telencephalon. PMID:23375746
Mechanisms of programmed DNA lesions and genomic instability in the immune system. PMID:23374339
A Parzen window-based approach for the detection of locally enriched transcription factor binding sites. PMID:23331723
Allele-specific transcriptional activity at type 2 diabetes-associated single nucleotide polymorphisms in regions of pancreatic islet open chromatin at the JAZF1 locus. PMID:23328127
Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures. PMID:23326246
Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules. PMID:23324445
Transcriptional dynamics elicited by a short pulse of notch activation involves feed-forward regulation by E(spl)/Hes genes. PMID:23300480
The underlying molecular and network level mechanisms in the evolution of robustness in gene regulatory networks. PMID:23300434
A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription. PMID:23282148
COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets. PMID:23272209
The twilight zone of cis element alignments. PMID:23268451
Gene expression levels of human shelterin complex and shelterin-associated factors regulated by the topoisomerase II inhibitors doxorubicin and etoposide in human cultured cells. PMID:23247865
Comprehensive human transcription factor binding site map for combinatory binding motifs discovery. PMID:23209563
STAT1:DNA sequence-dependent binding modulation by phosphorylation, protein:protein interactions and small-molecule inhibition. PMID:23180800
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. PMID:23180783
Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. PMID:23159369
The limits of de novo DNA motif discovery. PMID:23144830
Comparative genomics of neuroglobin reveals its early origins. PMID:23133533
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. PMID:23110901
Hepatocyte-specific deletion of hepatocyte nuclear factor-4α in adult mice results in increased hepatocyte proliferation. PMID:23104559
MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data. PMID:23093591
ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. PMID:23090257
Conserved epigenetic sensitivity to early life experience in the rat and human hippocampus. PMID:23045659
Research resource: interplay between the genomic and transcriptional networks of androgen receptor and estrogen receptor α in luminal breast cancer cells. PMID:23023562
Persistent androgen receptor-mediated transcription in castration-resistant prostate cancer under androgen-deprived conditions. PMID:23019221
Circuitry and dynamics of human transcription factor regulatory networks. PMID:22959076
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. PMID:22955990
Annotation of functional variation in personal genomes using RegulomeDB. PMID:22955989
Predicting cell-type-specific gene expression from regions of open chromatin. PMID:22955983
An expansive human regulatory lexicon encoded in transcription factor footprints. PMID:22955618
A high-coverage genome sequence from an archaic Denisovan individual. PMID:22936568
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. PMID:22936248
Regulatory elements of Caenorhabditis elegans ribosomal protein genes. PMID:22928635
Identification and analysis of pig chimeric mRNAs using RNA sequencing data. PMID:22925561
The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite. PMID:22906166
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. PMID:22898396
Why transcription factor binding sites are ten nucleotides long. PMID:22887818
Cell-type specificity of ChIP-predicted transcription factor binding sites. PMID:22863112
Multiple independent analyses reveal only transcription factors as an enriched functional class associated with microRNAs. PMID:22824421
Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. PMID:22785314
Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control. PMID:22759862
Developmental Coordination of Gene Expression between Synaptic Partners During GABAergic Circuit Assembly in Cerebellar Cortex. PMID:22754500
Towards a theoretical understanding of false positives in DNA motif finding. PMID:22738169
AKT3, ANGPTL4, eNOS3, and VEGFA associations with high altitude sickness in Han and Tibetan Chinese at the Qinghai-Tibetan Plateau. PMID:22729570
SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. PMID:22722849
VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. PMID:22693211
Evidence for directed evolution of larger size motif in Arabidopsis thaliana genome. PMID:22645502
New cis-regulatory elements in the Rht-D1b locus region of wheat. PMID:22592657
ELK1 uses different DNA binding modes to regulate functionally distinct classes of target genes. PMID:22589737
The dependence of expression of NF-κB-dependent genes: statistics and evolutionary conservation of control sequences in the promoter and in the 3' UTR. PMID:22577947
Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach. PMID:22558535
Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-α gene expression. PMID:22550178
Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding. PMID:22534400
Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. PMID:22482945
Intronic cis-regulatory modules mediate tissue-specific and microbial control of angptl4/fiaf transcription. PMID:22479192
Androgen receptor expression predicts breast cancer survival: the role of genetic and epigenetic events. PMID:22471922
Identification and analysis of conserved cis-regulatory regions of the MEIS1 gene. PMID:22448256
Regulatory versus coding signatures of natural selection in a candidate gene involved in the adaptive divergence of whitefish species pairs (Coregonus spp.). PMID:22408741
Deriving transcriptional programs and functional processes from gene expression databases. PMID:22408194
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. PMID:22397531
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity. PMID:22369666
Deciphering the Sox-Oct partner code by quantitative cooperativity measurements. PMID:22344693
Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. PMID:22328084
Quantification of transcription factor binding in cell extracts using an electrochemical, structure-switching biosensor. PMID:22313286
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq. PMID:22272348
Genome-wide progesterone receptor binding: cell type-specific and shared mechanisms in T47D breast cancer cells and primary leiomyoma cells. PMID:22272226
Genome-wide occupancy links Hoxa2 to Wnt-β-catenin signaling in mouse embryonic development. PMID:22223247
A model of genetic search for beneficial mutations: estimating the constructive capacities of mutagenesis. PMID:22212997
CLARE: Cracking the LAnguage of Regulatory Elements. PMID:22199387
A chromatin-modifying function of JNK during stem cell differentiation. PMID:22179133
Regulation of a duplicated locus: Drosophila sloppy paired is replete with functionally overlapping enhancers. PMID:22178246
Nrf2b, novel zebrafish paralog of oxidant-responsive transcription factor NF-E2-related factor 2 (NRF2). PMID:22174413
DNA-binding factors shape the mouse methylome at distal regulatory regions. PMID:22170606
Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets. PMID:22165960
Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function. PMID:22080862
Automated protein-DNA interaction screening of Drosophila regulatory elements. PMID:22037703
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. PMID:22037702
Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PMID:22028675
Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation. PMID:22028663
Tree-based position weight matrix approach to model transcription factor binding site profiles. PMID:21912677
Inactivation of a single copy of Crebbp selectively alters pre-mRNA processing in mouse hematopoietic stem cells. PMID:21901164
Discriminative prediction of mammalian enhancers from DNA sequence. PMID:21875935
Cooperative transcription factor associations discovered using regulatory variation. PMID:21828005
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. PMID:21821659
Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. PMID:21821656
ChIP-seq reveals cell type-specific binding patterns of BMP-specific Smads and a novel binding motif. PMID:21764776
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. PMID:21750106
Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers. PMID:21685454
Global identification of SMAD2 target genes reveals a role for multiple co-regulatory factors in zebrafish early gastrulas. PMID:21669877
Human teneurin-1 is a direct target of the homeobox transcription factor EMX2 at a novel alternate promoter. PMID:21651764
Gene coexpression clusters and putative regulatory elements underlying seed storage reserve accumulation in Arabidopsis. PMID:21635767
Genome-wide identification of conserved regulatory function in diverged sequences. PMID:21628450
Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation. PMID:21615920
TAFFEL: Independent Enrichment Analysis of gene sets. PMID:21592412
CpG islands and the regulation of transcription. PMID:21576262
Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators. PMID:21571218
A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites. PMID:21533218
Glucocorticoid receptor alpha isoform-selective regulation of antiapoptotic genes in osteosarcoma cells: a new mechanism for glucocorticoid resistance. PMID:21527497
Predicting promoter activities of primary human DNA sequences. PMID:21486745
Genome-wide tissue-specific occupancy of the Hox protein Ultrabithorax and Hox cofactor Homothorax in Drosophila. PMID:21483663
Hypoxia-inducible factor regulates expression of surfactant protein in alveolar type II cells in vitro. PMID:21454802
Azacytidine and decitabine induce gene-specific and non-random DNA demethylation in human cancer cell lines. PMID:21408221
Regulating Il9 transcription in T helper cells. PMID:21371941
Sex hormones in autism: androgens and estrogens differentially and reciprocally regulate RORA, a novel candidate gene for autism. PMID:21359227
An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq. PMID:21358819
De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PMID:21347314
Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants. PMID:21335608
Systematic search for enhancer elements and somatic allelic imbalance at seven low-penetrance colorectal cancer predisposition loci. PMID:21314996
G = MAT: linking transcription factor expression and DNA binding data. PMID:21297945
ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. PMID:21276248
A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation. PMID:21232107
Characterization of the core elements of the NF-κB signaling pathway of the sea anemone Nematostella vectensis. PMID:21189285
Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs. PMID:21187896
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. PMID:21183585
Predicting DNA-binding specificities of eukaryotic transcription factors. PMID:21152420
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. PMID:21106903
ATF3, a hub of the cellular adaptive-response network, in the pathogenesis of diseases: is modulation of inflammation a unifying component? PMID:21061913
Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position. PMID:21047394
Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. PMID:20876297
Processing and analyzing ChIP-seq data: from short reads to regulatory interactions. PMID:20861161
Identification of cis-regulatory elements in the mammalian genome: the cREMaG database. PMID:20824209
Global Egr1-miRNAs binding analysis in PMA-induced K562 cells using ChIP-Seq. PMID:20811575
ChIP-Seq identification of weakly conserved heart enhancers. PMID:20729851
Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels. PMID:20705733
Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny. PMID:20671200
Identification of E74-like factor 1 (ELF1) as a transcriptional regulator of the Hox cofactor MEIS1. PMID:20600580
Metamotifs--a generative model for building families of nucleotide position weight matrices. PMID:20579334
Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ. PMID:20552250
Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury. PMID:20534130
TFM-Explorer: mining cis-regulatory regions in genomes. PMID:20522509
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. PMID:20517297
Genome-wide identification of new Wnt/beta-catenin target genes in the human genome using CART method. PMID:20515496
A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PMID:20505756
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. PMID:20478823
Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis. PMID:20460467
A cis-regulatory signature for chordate anterior neuroectodermal genes. PMID:20419150
MochiView: versatile software for genome browsing and DNA motif analysis. PMID:20409324
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. PMID:20378718
Negative regulation of the oncogenic transcription factor FoxM1 by thiazolidinediones and mithramycin. PMID:20372080
3-methylcholanthrene induces differential recruitment of aryl hydrocarbon receptor to human promoters. PMID:20348232
A Study of the Distribution of Phylogenetically Conserved Blocks within Clusters of Mammalian Homeobox Genes. PMID:20209015
Genome-wide transcription factor binding site/promoter databases for the analysis of gene sets and co-occurrence of transcription factor binding motifs. PMID:20193056
Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia. PMID:20193046
Using Trawler_standalone to discover overrepresented motifs in DNA and RNA sequences derived from various experiments including chromatin immunoprecipitation. PMID:20134431
The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. PMID:20123907
iMotifs: an integrated sequence motif visualization and analysis environment. PMID:20106815
Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans. PMID:20100800
A novel alignment-free method for comparing transcription factor binding site motifs. PMID:20098703
Genome-wide prediction of transcription factor binding sites using an integrated model. PMID:20096096
Finding Occurrences of Relevant Functional Elements in Genomic Signatures. PMID:20046539
Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis. PMID:20003344
Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. PMID:19969543
A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data. PMID:19956545
Long-range transcriptional control of progesterone receptor gene expression. PMID:19952285
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. PMID:19941641
Adenovirus VA RNA-derived miRNAs target cellular genes involved in cell growth, gene expression and DNA repair. PMID:19933264
Discovery of regulatory elements is improved by a discriminatory approach. PMID:19911049
Knowledge-based data analysis comes of age. PMID:19854753
Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. PMID:19853570
Exhaustive search for over-represented DNA sequence motifs with CisFinder. PMID:19740934
CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses. PMID:19736212
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach. PMID:19604364
Word-based characterization of promoters involved in human DNA repair pathways. PMID:19594877
Dioxin increases the interaction between aryl hydrocarbon receptor and estrogen receptor alpha at human promoters. PMID:19574409
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation. PMID:19558665
A combinatorial mechanism for determining the specificity of E2F activation and repression. PMID:19543322
Functional and comparative genomics analyses of pmp22 in medaka fish. PMID:19534778
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes. PMID:19534755
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. PMID:19487240
Transcriptional features of genomic regulatory blocks. PMID:19374772
The interplay between transcription factors and microRNAs in genome-scale regulatory networks. PMID:19274664
Biological convergence of cancer signatures. PMID:19229342
Lentiviral transfection of ependymal primary cultures facilitates the characterisation of kinocilia-specific promoters. PMID:19191024
Caenorhabditis elegans cisRED: a catalogue of conserved genomic elements. PMID:19151087
A transcription factor affinity-based code for mammalian transcription initiation. PMID:19141595
Compo: composite motif discovery using discrete models. PMID:19063744
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. PMID:19036138
Multigenome DNA sequence conservation identifies Hox cis-regulatory elements. PMID:18981268
An optimized procedure for the design and evaluation of Ecotilling assays. PMID:18973671
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. PMID:18842628
Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock. PMID:18815372
Identification of Arx transcriptional targets in the developing basal forebrain. PMID:18799476
Modeling ChIP sequencing in silico with applications. PMID:18725927
The commensal Streptococcus salivarius K12 downregulates the innate immune responses of human epithelial cells and promotes host-microbe homeostasis. PMID:18625732
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. PMID:18585359
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species. PMID:18453628
Asap: a framework for over-representation statistics for transcription factor binding sites. PMID:18286180
The genome landscape of ERalpha- and ERbeta-binding DNA regions. PMID:18272478
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles PubMed citations: 372.

372 articles citing: JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

Regulatory patterns analysis of transcription factor binding site clustered regions and identification of key genes in endometrial cancer. PMID:35222842
Genome-Wide Prediction of Transcription Start Sites in Conifers. PMID:35163661
Molecular Pathways Modulating Sensory Hair Cell Regeneration in Adult Mammalian Cochleae: Progress and Perspectives. PMID:35008497
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. PMID:34850907
Nuclear transporter Importin-13 plays a key role in the oxidative stress transcriptional response. PMID:34625540
ETS1, ELK1, and ETV4 Transcription Factors Regulate Angiopoietin-1 Signaling and the Angiogenic Response in Endothelial Cells. PMID:34381375
Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. PMID:34208629
Epigenetic evidence of an Ac/Dc axis by VPA and SAHA. PMID:33743782
Association of hsa-mir-328-3p Expression in Whole Blood With Optical Density of Retinal Pigment Epithelial Cells. PMID:33622875
Phenotypic Mapping of Pathologic Cross-Talk between Glioblastoma and Innate Immune Cells by Synthetic Genetic Tracing. PMID:33361384
A Multi-Source Data Fusion Framework for Revealing the Regulatory Mechanism of Breast Cancer Immune Evasion. PMID:33304391
CD36 upregulates DEK transcription and promotes cell migration and invasion via GSK-3β/β-catenin-mediated epithelial-to-mesenchymal transition in gastric cancer. PMID:33232276
Tau Pathology Drives Dementia Risk-Associated Gene Networks toward Chronic Inflammatory States and Immunosuppression. PMID:33207193
Nuclear FOXP3 inhibits tumor growth and induced apoptosis in hepatocellular carcinoma by targeting c-Myc. PMID:33116119
Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss. PMID:32816922
Runx2+ Niche Cells Maintain Incisor Mesenchymal Tissue Homeostasis through IGF Signaling. PMID:32783935
The RNA exosome shapes the expression of key protein-coding genes. PMID:32710631
Nurr1 performs its anti-inflammatory function by regulating RasGRP1 expression in neuro-inflammation. PMID:32612143
CSA: a web service for the complete process of ChIP-Seq analysis. PMID:31874601
The CLN3 gene and protein: What we know. PMID:31568712
Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks. PMID:31477008
Testosterone Deficiency Caused by Castration Modulates Mitochondrial Biogenesis Through the AR/PGC1α/TFAM Pathway. PMID:31191617
RETRACTED ARTICLE: Selected TLR7/8 agonist and type I interferon (IFN-α) cooperatively redefine the microglia transcriptome. PMID:31190206
An Exploration Into Improving DNA Motif Inference by Looking for Highly Conserved Core Regions. PMID:31008453
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data. PMID:30962623
DNA-protein interaction: identification, prediction and data analysis. PMID:30915687
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features. PMID:30727967
Interpretation of an individual functional genomics experiment guided by massive public data. PMID:30478325
Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians. PMID:30181897
Novel lymphoid enhancer-binding factor 1-cytoglobin axis promotes extravasation of osteosarcoma cells into the lungs. PMID:29927026
Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data. PMID:29900118
Detecting Differential Transcription Factor Activity from ATAC-Seq Data. PMID:29748466
High-Resolution Mapping and Dynamics of the Transcriptome, Transcription Factors, and Transcription Co-Factor Networks in Classically and Alternatively Activated Macrophages. PMID:29403501
Loss of Angelman Syndrome Protein E6AP Disrupts a Novel Antagonistic Estrogen-Retinoic Acid Transcriptional Crosstalk in Neurons. PMID:29388081
Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes. PMID:29363429
Global mapping of transcription factor motifs in human aging. PMID:29293662
Insulin-like growth factor 2 expression in prostate cancer is regulated by promoter-specific methylation. PMID:29239100
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. PMID:29140473
Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease. PMID:29138457
Functional polymorphism of the renalase gene is associated with cardiac hypertrophy in female patients with aortic stenosis. PMID:29065134
Intragenic Enhancers Attenuate Host Gene Expression. PMID:28985501
RNA sequencing reveals resistance of TLR4 ligand-activated microglial cells to inflammation mediated by the selective jumonji H3K27 demethylase inhibitor. PMID:28747667
Association analyses based on false discovery rate implicate new loci for coronary artery disease. PMID:28714975
In silico pathway analysis and tissue specific cis-eQTL for colorectal cancer GWAS risk variants. PMID:28506205
A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model. PMID:28497059
Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data. PMID:28472398
ConTra v3: a tool to identify transcription factor binding sites across species, update 2017. PMID:28472390
Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PMID:28414715
E6-Associated Protein Dependent Estrogen Receptor Regulation of Protein Kinase A Regulatory Subunit R2A Expression in Neuroblastoma. PMID:28214999
Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. PMID:28165450
Inferring condition-specific targets of human TF-TF complexes using ChIP-seq data. PMID:28068916
iFORM: Incorporating Find Occurrence of Regulatory Motifs. PMID:27992540
Brain transcriptome atlases: a computational perspective. PMID:27909802
DNA methylation patterns associated with oxidative stress in an ageing population. PMID:27884142
Evaluating tools for transcription factor binding site prediction. PMID:27806697
Distinct Cell Stress Responses Induced by ATP Restriction in Quiescent Human Fibroblasts. PMID:27757122
Drought response transcriptomes are altered in poplar with reduced tonoplast sucrose transporter expression. PMID:27641356
SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules. PMID:27637070
Genome-wide identification and characterisation of HOT regions in the human genome. PMID:27633377
Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. PMID:27585846
PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina. PMID:27556059
CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design. PMID:27487245
Prediction and Validation of Transcription Factors Modulating the Expression of Sestrin3 Gene Using an Integrated Computational and Experimental Approach. PMID:27466818
Transcriptome sequencing wide functional analysis of human mesenchymal stem cells in response to TLR4 ligand. PMID:27444640
Genome-Wide Meta-Analyses of Breast, Ovarian, and Prostate Cancer Association Studies Identify Multiple New Susceptibility Loci Shared by at Least Two Cancer Types. PMID:27432226
Transcriptome sequencing reveals that LPS-triggered transcriptional responses in established microglia BV2 cell lines are poorly representative of primary microglia. PMID:27400875
A PBX1 transcriptional network controls dopaminergic neuron development and is impaired in Parkinson's disease. PMID:27354364
MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis. PMID:27302134
Characterization of a New Pink-Fruited Tomato Mutant Results in the Identification of a Null Allele of the SlMYB12 Transcription Factor. PMID:27208285
Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots. PMID:27195960
Composing a Tumor Specific Bacterial Promoter. PMID:27171245
HIV-1 Promoter Single Nucleotide Polymorphisms Are Associated with Clinical Disease Severity. PMID:27100290
p53 transcriptional programs in B cells upon exposure to genotoxic stress in vivo: Computational analysis of next-generation sequencing data. PMID:26981355
Constructing 3D interaction maps from 1D epigenomes. PMID:26960733
RNA Sequencing Reveals the Alteration of the Expression of Novel Genes in Ethanol-Treated Embryoid Bodies. PMID:26930486
A Systems-Level Analysis of the Peripheral Nerve Intrinsic Axonal Growth Program. PMID:26898779
Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva. PMID:26896950
Evolutionary Footprints of Short Tandem Repeats in Avian Promoters. PMID:26766026
Research Resource: Hormones, Genes, and Athleticism: Effect of Androgens on the Avian Muscular Transcriptome. PMID:26745669
Bioinformatic landscapes for plant transcription factor system research. PMID:26719053
Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors. PMID:26673794
Control of developmentally primed erythroid genes by combinatorial co-repressor actions. PMID:26593974
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. PMID:26586237
Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain. PMID:26575220
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. PMID:26531826
Temporal and spatial control of gene expression in horticultural crops. PMID:26504550
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. PMID:26502339
A Statistical Framework for the Analysis of ChIP-Seq Data. PMID:26478641
Absence of canonical marks of active chromatin in developmentally regulated genes. PMID:26280901
A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors. PMID:26272509
Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal. PMID:26267829
Heterogeneous Effects of Direct Hypoxia Pathway Activation in Kidney Cancer. PMID:26262842
Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus. PMID:26220934
A microfluidic device for epigenomic profiling using 100 cells. PMID:26214128
Transcriptome sequencing of microglial cells stimulated with TLR3 and TLR4 ligands. PMID:26159724
Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins. PMID:26134422
Nuclear respiratory factor 2 induces SIRT3 expression. PMID:26109058
Identification of novel Fgf enhancers and their role in dental evolution. PMID:26086993
Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites. PMID:26076233
Kinase-independent role of cyclin D1 in chromosomal instability and mammary tumorigenesis. PMID:25940700
The Dlx5 and Foxg1 transcription factors, linked via miRNA-9 and -200, are required for the development of the olfactory and GnRH system. PMID:25937343
Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data. PMID:25927199
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. PMID:25925574
Understanding multicellular function and disease with human tissue-specific networks. PMID:25915600
Compound mouse mutants of bZIP transcription factors Mafg and Mafk reveal a regulatory network of non-crystallin genes associated with cataract. PMID:25896808
Global gene expression profiling of brown to white adipose tissue transformation in sheep reveals novel transcriptional components linked to adipose remodeling. PMID:25887780
Dual RNA sequencing reveals the expression of unique transcriptomic signatures in lipopolysaccharide-induced BV-2 microglial cells. PMID:25811458
A family of transposable elements co-opted into developmental enhancers in the mouse neocortex. PMID:25806706
SLFN11 Is a Transcriptional Target of EWS-FLI1 and a Determinant of Drug Response in Ewing Sarcoma. PMID:25779942
Regulatory circuit of PKM2/NF-κB/miR-148a/152-modulated tumor angiogenesis and cancer progression. PMID:25703326
An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape. PMID:25682954
Autophagy Regulatory Network - a systems-level bioinformatics resource for studying the mechanism and regulation of autophagy. PMID:25635527
Enhancer evolution across 20 mammalian species. PMID:25635462
The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes. PMID:25518738
Loss of the Notch effector RBPJ promotes tumorigenesis. PMID:25512468
p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response. PMID:25486198
Epigenome-guided analysis of the transcriptome of plaque macrophages during atherosclerosis regression reveals activation of the Wnt signaling pathway. PMID:25474352
Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee. PMID:25453090
Estimating binding properties of transcription factors from genome-wide binding profiles. PMID:25432957
Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses. PMID:25392756
A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components. PMID:25374456
Oncogenic Ras inhibits IRF1 to promote viral oncolysis. PMID:25347735
Abundance, arrangement, and function of sequence motifs in the chicken promoters. PMID:25318583
Dissecting the mechanism of carotid atherosclerosis from the perspective of regulation. PMID:25318463
Coregulated expression of the Na+/phosphate Pho89 transporter and Ena1 Na+-ATPase allows their functional coupling under high-pH stress. PMID:25266663
High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions. PMID:25259795
MACE: model based analysis of ChIP-exo. PMID:25249628
Determination and inference of eukaryotic transcription factor sequence specificity. PMID:25215497
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. PMID:25208583
Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network. PMID:25199827
Differential motif enrichment analysis of paired ChIP-seq experiments. PMID:25179504
An otx/nodal regulatory signature for posterior neural development in ascidians. PMID:25121599
Transcriptional regulation of the tumor suppressor FHL2 by p53 in human kidney and liver cells. PMID:25121502
Bioinformatics analysis of biomarkers and transcriptional factor motifs in Down syndrome. PMID:25118625
Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets. PMID:25070602
TGFβ loss activates ADAMTS-1-mediated EGF-dependent invasion in a model of esophageal cell invasion. PMID:25064463
iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PMID:25058159
Probing the effect of promoters on noise in gene expression using thousands of designed sequences. PMID:25030889
Conservation and divergence of transcriptional coregulations between box C/D snoRNA and ribosomal protein genes in Ascomycota. PMID:25002674
Large-scale investigation of human TF-miRNA relations based on coexpression profiles. PMID:24995316
Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2. PMID:24990076
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. PMID:24927817
A general pairwise interaction model provides an accurate description of in vivo transcription factor binding sites. PMID:24926895
Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts. PMID:24922324
On the identification of potential regulatory variants within genome wide association candidate SNP sets. PMID:24920305
Cellular dissection of psoriasis for transcriptome analyses and the post-GWAS era. PMID:24885462
Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells. PMID:24885402
COUGER--co-factors associated with uniquely-bound genomic regions. PMID:24861628
Motif enrichment tool. PMID:24860165
The systemic amyloid precursor transthyretin (TTR) behaves as a neuronal stress protein regulated by HSF1 in SH-SY5Y human neuroblastoma cells and APP23 Alzheimer's disease model mice. PMID:24849358
RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). PMID:24779366
Nucleosome regulatory dynamics in response to TGFβ. PMID:24771338
Determining causality and consequence of expression quantitative trait loci. PMID:24770875
Urothelial carcinoma associated 1 is a hypoxia-inducible factor-1α-targeted long noncoding RNA that enhances hypoxic bladder cancer cell proliferation, migration, and invasion. PMID:24737584
Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation. PMID:24682824
MutationTaster2: mutation prediction for the deep-sequencing age. PMID:24681721
Signaling by IL-6 promotes alternative activation of macrophages to limit endotoxemia and obesity-associated resistance to insulin. PMID:24681566
Two enhancers control transcription of Drosophila muscleblind in the embryonic somatic musculature and in the central nervous system. PMID:24667536
Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis. PMID:24655370
Dissecting the causal genetic mechanisms of coronary heart disease. PMID:24623178
Transcriptional enhancers: from properties to genome-wide predictions. PMID:24614317
A compensatory role of NF-κB to p53 in response to 5-FU-based chemotherapy for gastric cancer cell lines. PMID:24587255
DLX5, FGF8 and the Pin1 isomerase control ΔNp63α protein stability during limb development: a regulatory loop at the basis of the SHFM and EEC congenital malformations. PMID:24569166
Characterizing dynamic regulatory programs in mouse lung development and their potential association with tumourigenesis via miRNA-TF-mRNA circuits. PMID:24564886
Identification of novel motif patterns to decipher the promoter architecture of co-expressed genes in Arabidopsis thaliana. PMID:24555803
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
Two independent transcription initiation codes overlap on vertebrate core promoters. PMID:24531765
Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data. PMID:24499934
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data. PMID:24472686
Identifying and mapping cell-type-specific chromatin programming of gene expression. PMID:24469817
Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution. PMID:24453983
A common functional regulatory variant at a type 2 diabetes locus upregulates ARAP1 expression in the pancreatic beta cell. PMID:24439111
Profiling, Bioinformatic, and Functional Data on the Developing Olfactory/GnRH System Reveal Cellular and Molecular Pathways Essential for This Process and Potentially Relevant for the Kallmann Syndrome. PMID:24427155
Functional characterization of a bidirectional plant promoter from cotton leaf curl Burewala virus using an Agrobacterium-mediated transient assay. PMID:24424501
Sho-saiko-to, a traditional herbal medicine, regulates gene expression and biological function by way of microRNAs in primary mouse hepatocytes. PMID:24410935
Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns. PMID:24395799
Reverse engineering the neuroblastoma regulatory network uncovers MAX as one of the master regulators of tumor progression. PMID:24349289
TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors. PMID:24349230
Progesterone receptor assembly of a transcriptional complex along with activator protein 1, signal transducer and activator of transcription 3 and ErbB-2 governs breast cancer growth and predicts response to endocrine therapy. PMID:24345432
Fine mapping of the celiac disease-associated LPP locus reveals a potential functional variant. PMID:24334606
Ensembl 2014. PMID:24316576
PKCε signalling activates ERK1/2, and regulates aggrecan, ADAMTS5, and miR377 gene expression in human nucleus pulposus cells. PMID:24312401
Genome-wide analysis of coordinated transcript abundance during seed development in different Brassica rapa morphotypes. PMID:24289287
Parallel evolution of chordate cis-regulatory code for development. PMID:24282393
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites. PMID:24271386
Saccharomyces genome database provides new regulation data. PMID:24265222
Modulation of epidermal transcription circuits in psoriasis: new links between inflammation and hyperproliferation. PMID:24260178
Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets. PMID:24217919
TFBSshape: a motif database for DNA shape features of transcription factor binding sites. PMID:24214955
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. PMID:24194598
Identification of novel microRNAs in primates by using the synteny information and small RNA deep sequencing data. PMID:24135875
Plant promoters: an approach of structure and function. PMID:24122284
Androgen regulation of the TMPRSS2 gene and the effect of a SNP in an androgen response element. PMID:24109594
De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. PMID:24097433
pLogo: a probabilistic approach to visualizing sequence motifs. PMID:24097270
Flanking sequence context-dependent transcription factor binding in early Drosophila development. PMID:24093548
Jaccard index based similarity measure to compare transcription factor binding site models. PMID:24074225
Cycles in spatial and temporal chromosomal organization driven by the circadian clock. PMID:24056944
miREval 2.0: a web tool for simple microRNA prediction in genome sequences. PMID:24048357
Topology of molecular interaction networks. PMID:24041013
The next generation of transcription factor binding site prediction. PMID:24039567
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. PMID:24002785
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs. PMID:23958307
Early phase of plasticity-related gene regulation and SRF dependent transcription in the hippocampus. PMID:23935853
Dissecting the psoriasis transcriptome: inflammatory- and cytokine-driven gene expression in lesions from 163 patients. PMID:23915137
The BTB-zinc finger transcription factor abrupt acts as an epithelial oncogene in Drosophila melanogaster through maintaining a progenitor-like cell state. PMID:23874226
Trans-ancestral studies fine map the SLE-susceptibility locus TNFSF4. PMID:23874208
A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. PMID:23873954
Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. PMID:23851456
DNA methylation restricts lineage-specific functions of transcription factor Gata4 during embryonic stem cell differentiation. PMID:23825962
DNA motif elucidation using belief propagation. PMID:23814189
Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency. PMID:23798425
Genome Maps, a new generation genome browser. PMID:23748955
PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. PMID:23748563
De novo mutations in the genome organizer CTCF cause intellectual disability. PMID:23746550
Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by a Marek's disease virus oncoprotein, Meq. PMID:23740999
Evolutionary change driven by metal exposure as revealed by coding SNP genome scan in wild yellow perch (Perca flavescens). PMID:23722603
NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. PMID:23710289
Computational identification of active enhancers in model organisms. PMID:23685394
Age-specific signatures of glioblastoma at the genomic, genetic, and epigenetic levels. PMID:23658659
Twine: display and analysis of cis-regulatory modules. PMID:23658420
Candidate gene association studies: a comprehensive guide to useful in silico tools. PMID:23656885
D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements. PMID:23617301
NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. PMID:23595228
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. PMID:23586463
Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis. PMID:23560912
C/EBPα is required for development of dendritic cell progenitors. PMID:23547051
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. PMID:23482648
Identification of candidate transcription factor binding sites in the cattle genome. PMID:23433959
An integrated approach to characterize transcription factor and microRNA regulatory networks involved in Schwann cell response to peripheral nerve injury. PMID:23387820
Robust shifts in S100a9 expression with aging: a novel mechanism for chronic inflammation. PMID:23386971
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
BMP-mediated functional cooperation between Dlx5;Dlx6 and Msx1;Msx2 during mammalian limb development. PMID:23382810
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
Genetic architecture of gene expression in the chicken. PMID:23324119
MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis. PMID:23323883
Spatial promoter recognition signatures may enhance transcription factor specificity in yeast. PMID:23320104
Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. PMID:23295670
Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites. PMID:23281809
A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types. PMID:23271069
Searching for transcription factor binding sites in vector spaces. PMID:23244338
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. PMID:23228284
Nuclear RNA sequencing of the mouse erythroid cell transcriptome. PMID:23209567
Ensembl 2013. PMID:23203987
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. PMID:23203868
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. PMID:23197657
Computational discovery of regulatory elements in a continuous expression space. PMID:23186104
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. PMID:23175603
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. PMID:23161675
Genome-wide chromatin remodeling identified at GC-rich long nucleosome-free regions. PMID:23144837
Novel Foxo1-dependent transcriptional programs control T(reg) cell function. PMID:23135404
Global gene expression of the inner cell mass and trophectoderm of the bovine blastocyst. PMID:23126590
Overlapping ETS and CRE Motifs ((G/C)CGGAAGTGACGTCA) preferentially bound by GABPα and CREB proteins. PMID:23050235
Three enhancements to the inference of statistical protein-DNA potentials. PMID:23042633
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. PMID:23034120
Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data. PMID:23029415
Cooperativity of stress-responsive transcription factors in core hypoxia-inducible factor binding regions. PMID:23029193
Computational prediction of polycomb-associated long non-coding RNAs. PMID:23028655
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets. PMID:22973536
Comparative genomics-based identification and analysis of cis-regulatory elements. PMID:22956093
Systematic localization of common disease-associated variation in regulatory DNA. PMID:22955828
Genome-wide in silico prediction of gene expression. PMID:22954627
Increasing coverage of transcription factor position weight matrices through domain-level homology. PMID:22952610
Analysis of variation at transcription factor binding sites in Drosophila and humans. PMID:22950968
TFinDit: transcription factor-DNA interaction data depository. PMID:22943312
Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. PMID:22941648
Mitochondrial DNA copy number is regulated in a tissue specific manner by DNA methylation of the nuclear-encoded DNA polymerase gamma A. PMID:22941637
Improved predictions of transcription factor binding sites using physicochemical features of DNA. PMID:22923524
Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics. PMID:22915576
Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites. PMID:22913572
HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions. PMID:22900683
An integrative computational approach to effectively guide experimental identification of regulatory elements in promoters. PMID:22897887
Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data. PMID:22844240
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. PMID:22836136
Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome. PMID:22829947
The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding. PMID:22827163
Identification and dissection of four major QTL affecting milk fat content in the German Holstein-Friesian population. PMID:22792397
POWRS: position-sensitive motif discovery. PMID:22792292
Large-scale computational identification of regulatory SNPs with rSNP-MAPPER. PMID:22759655
Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots. PMID:22759569
Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2. PMID:22737085
RBFOX1 regulates both splicing and transcriptional networks in human neuronal development. PMID:22730494
i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. PMID:22718975
The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops. PMID:22641035
Evolution of a tissue-specific silencer underlies divergence in the expression of pax2 and pax8 paralogues. PMID:22617288
Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach. PMID:22558535
Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. PMID:22537144
Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PMID:22532803
Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. PMID:22510988
Multidimensional regulation of gene expression in the C. elegans embryo. PMID:22508763
Improved models for transcription factor binding site identification using nonindependent interactions. PMID:22505627
System approaches reveal the molecular networks involved in neural stem cell differentiation. PMID:22492180
The transcription factor encyclopedia. PMID:22458515
Antagonistic regulation of apoptosis and differentiation by the Cut transcription factor represents a tumor-suppressing mechanism in Drosophila. PMID:22438831
Meta-profiles of gene expression during aging: limited similarities between mouse and human and an unexpectedly decreased inflammatory signature. PMID:22413003
A Whole-Chromosome Analysis of Meiotic Recombination in Drosophila melanogaster. PMID:22384403
pcaGoPromoter--an R package for biological and regulatory interpretation of principal components in genome-wide gene expression data. PMID:22384239
Genome-wide repression of NF-κB target genes by transcription factor MIBP1 and its modulation by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase. PMID:22294689
Use of ChIP-Seq data for the design of a multiple promoter-alignment method. PMID:22230796
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. PMID:22228832
MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets. PMID:22210894
Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells. PMID:22210892
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. PMID:22208852
Promoter architecture of mouse olfactory receptor genes. PMID:22194471
Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices. PMID:22187154
Regulation of a duplicated locus: Drosophila sloppy paired is replete with functionally overlapping enhancers. PMID:22178246
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. PMID:22156162
A systematic analysis of the 3'UTR of HNF4A mRNA reveals an interplay of regulatory elements including miRNA target sites. PMID:22140441
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species. PMID:22140105
The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites. PMID:22121218
Ensembl 2012. PMID:22086963
AnimalTFDB: a comprehensive animal transcription factor database. PMID:22080564
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. PMID:22080467
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. PMID:22064851
SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. PMID:22055187
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. PMID:22051799
Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. PMID:22047616
A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. PMID:22022263
Chipster: user-friendly analysis software for microarray and other high-throughput data. PMID:21999641
Identification of cis-regulatory sequence variations in individual genome sequences. PMID:21989199
Visualization and exploration of conserved regulatory modules using ReXSpecies 2. PMID:21942985
Systematic clustering of transcription start site landscapes. PMID:21887249
The NFI-Regulome Database: A tool for annotation and analysis of control regions of genes regulated by Nuclear Factor I transcription factors. PMID:21884625
Cistrome: an integrative platform for transcriptional regulation studies. PMID:21859476
AlleleSeq: analysis of allele-specific expression and binding in a network framework. PMID:21811232
Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. PMID:21779159
Identifying functional single nucleotide polymorphisms in the human CArGome. PMID:21771879
Integration of genome-wide computation DRE search, AhR ChIP-chip and gene expression analyses of TCDD-elicited responses in the mouse liver. PMID:21762485
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. PMID:21750106
Tissue-specific prediction of directly regulated genes. PMID:21724591
RSAT 2011: regulatory sequence analysis tools. PMID:21715389
MotifClick: prediction of cis-regulatory binding sites via merging cliques. PMID:21679436
Inflammatory gene regulatory networks in amnion cells following cytokine stimulation: translational systems approach to modeling human parturition. PMID:21655103
Cell type-specific target selection by combinatorial binding of Smad2/3 proteins and hepatocyte nuclear factor 4alpha in HepG2 cells. PMID:21646355
RAD21 cooperates with pluripotency transcription factors in the maintenance of embryonic stem cell identity. PMID:21589869
ConTra v2: a tool to identify transcription factor binding sites across species, update 2011. PMID:21576231
Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. PMID:21572415
mirConnX: condition-specific mRNA-microRNA network integrator. PMID:21558324
An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. PMID:21556064
Improved similarity scores for comparing motifs. PMID:21543443
MEME-ChIP: motif analysis of large DNA datasets. PMID:21486936
Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. PMID:21415370
MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. PMID:21375730
Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1. PMID:21324158
Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. PMID:21321018
Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing. PMID:21310711
The nephrogenic potential of the transcription factors osr1, osr2, hnf1b, lhx1 and pax8 assessed in Xenopus animal caps. PMID:21281489
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PMID:21249180
Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation. PMID:21235772
Systematic characterization of protein-DNA interactions. PMID:21207099
Evolution of gene regulation of pluripotency--the case for wiki tracks at genome browsers. PMID:21190561
Using bioinformatics to predict the functional impact of SNVs. PMID:21159622
Studying the evolution of promoter sequences: a waiting time problem. PMID:21128851
Computational biology for ageing. PMID:21115530
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. PMID:21097781
A polymorphism in the HLA-DPB1 gene is associated with susceptibility to multiple sclerosis. PMID:21049023
Ensembl 2011. PMID:21045057
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. PMID:21045055
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. PMID:21037262
RBPDB: a database of RNA-binding specificities. PMID:21036867
Scaffolding a Caenorhabditis nematode genome with RNA-seq. PMID:20980554
Genetic and molecular functional characterization of variants within TNFSF13B, a positional candidate preeclampsia susceptibility gene on 13q. PMID:20927378
Theoretical and empirical quality assessment of transcription factor-binding motifs. PMID:20923783
Genetic determinants of HSP70 gene expression following heat shock. PMID:20876613
Conserved proximal promoter elements control repulsive guidance molecule c/hemojuvelin (Hfe2) gene transcription in skeletal muscle. PMID:20858542
Protein kinase target discovery from genome-wide messenger RNA expression profiling. PMID:20687179
Genomic repertoires of DNA-binding transcription factors across the tree of life. PMID:20675356
PriorsEditor: a tool for the creation and use of positional priors in motif discovery. PMID:20628076
Dual-functioning transcription factors in the developmental gene network of Drosophila melanogaster. PMID:20594356
Metamotifs--a generative model for building families of nucleotide position weight matrices. PMID:20579334
TransFind--predicting transcriptional regulators for gene sets. PMID:20511592
Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data. PMID:20435683