HOmo sapiens transcription factor COmprehensive MOdel COllection
Names
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HOmo sapiens transcription factor COmprehensive MOdel COllection
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
HOCOMOCO
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:29.851370
hocomoco
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:29.851370
Names
More detailed information about this field from each metasource.
HOmo sapiens transcription factor COmprehensive MOdel COllection
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
HOCOMOCO
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:29.851370
hocomoco
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:29.851370
Other names: HOCOMOCO, hocomoco
Names
More detailed information about this field from each metasource.
HOmo sapiens transcription factor COmprehensive MOdel COllection
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
HOCOMOCO
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:29.851370
hocomoco
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:29.851370
HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v10 provides transcription factor (TF) binding models for 601 human and 396 mouse TFs. In addition to basic mononucleotide position weight matrices (PWMs), HOCOMOCO provides a set of dinucleotide position weight matrices based on ChIP-Seq data. All the models were produced by the ChIPMunk motif discovery tool. Models are manually curated with assigning model quality ratings based upon benchmark studies or inherited from HOCOMOCO v9. ChIP-Seq data for motif discovery was extracted from GTRD database of BioUML platform, that also provides an interface for motif finding (sequence scanning) with HOCOMOCO models. Other sequences of TF binding DNA regions were collected from existing databases and other public data. An appropriate TFBS model was selected for each TF, with similar models selected for related TFs. All TFBS models and initial binding segments data used for motif discovery were mapped to UniPROT IDs. TF coding genes are linked with GeneCards entries. DNA binding domains are linked with TF class database.
Description
More detailed information about this field from each metasource.
HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v10 provides transcription factor (TF) binding models for 601 human and 396 mouse TFs. In addition to basic mononucleotide position weight matrices (PWMs), HOCOMOCO provides a set of dinucleotide position weight matrices based on ChIP-Seq data. All the models were produced by the ChIPMunk motif discovery tool. Models are manually curated with assigning model quality ratings based upon benchmark studies or inherited from HOCOMOCO v9. ChIP-Seq data for motif discovery was extracted from GTRD database of BioUML platform, that also provides an interface for motif finding (sequence scanning) with HOCOMOCO models. Other sequences of TF binding DNA regions were collected from existing databases and other public data. An appropriate TFBS model was selected for each TF, with similar models selected for related TFs. All TFBS models and initial binding segments data used for motif discovery were mapped to UniPROT IDs. TF coding genes are linked with GeneCards entries. DNA binding domains are linked with TF class database.
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
HOmo sapiens COmprehensive MOdel COllection of hand-curated transcription factor binding site models
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
HOmo sapiens transcription factor COmprehensive MOdel COllection contains transcription factor (TF) binding models (motifs) as position weight matrices for human and mouse transcription factors.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:29.851370
Webpage:
http://hocomoco.autosome.ru/Webpage
More detailed information about this field from each metasource.
http://hocomoco.autosome.ru/
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
https://hocomoco.autosome.org
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:29.851370
http://autosome.ru/HOCOMOCO
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence URL
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https://creativecommons.org/licenses/by-nc/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
(7)
Publications
More detailed information about this field from each metasource.
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
PMID: 29140464
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
PMID: 23175603
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Deep and wide digging for binding motifs in ChIP-Seq data
PMID: 20736340
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites
PMID: 23427986
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Jaccard index based similarity measure to compare transcription factor binding site models
PMID: 24074225
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gks1089
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkx1106
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:29.851370
Publications
More detailed information about this field from each metasource.
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
PMID: 29140464
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
PMID: 23175603
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Deep and wide digging for binding motifs in ChIP-Seq data
PMID: 20736340
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites
PMID: 23427986
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Jaccard index based similarity measure to compare transcription factor binding site models
PMID: 24074225
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gks1089
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkx1106
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:29.851370
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HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
PubMed citations: 231.
231 articles citing: HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
Functional Genomics Analysis to Disentangle the Role of Genetic Variants in Major Depression. PMID:35886042
Discovering the drivers of clonal hematopoiesis. PMID:35871184
DESSO-DB: A web database for sequence and shape motif analyses and identification. PMID:35782725
The hypoxia-induced changes in miRNA-mRNA in RNA-induced silencing complexes and HIF-2 induced miRNAs in human endothelial cells. PMID:35713587
Ranking reprogramming factors for cell differentiation. PMID:35710610
Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome. PMID:35681170
ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge's disease. PMID:35672450
Integrating 3D genomic and epigenomic data to enhance target gene discovery and drug repurposing in transcriptome-wide association studies. PMID:35672318
EHF is a novel regulator of cellular redox metabolism and predicts patient prognosis in HNSCC. PMID:35664541
FABIAN-variant: predicting the effects of DNA variants on transcription factor binding. PMID:35639768
Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning. PMID:35606422
3DCoop: An approach for computational inference of cell-type-specific transcriptional regulators cooperation in 3D chromatin. PMID:35600920
Compatibility rules of human enhancer and promoter sequences. PMID:35594906
Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish. PMID:35551306
Reorganization of postmitotic neuronal chromatin accessibility for maturation of serotonergic identity. PMID:35471146
A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation. PMID:35440565
Cooperative interaction between ERα and the EMT-inducer ZEB1 reprograms breast cancer cells for bone metastasis. PMID:35440541
Machine Learning Prediction of Non-Coding Variant Impact in Human Retinal cis-Regulatory Elements. PMID:35435921
Multi-omics protein-coding units as massively parallel Bayesian networks: Empirical validation of causality structure. PMID:35355520
Nuclear receptor activation shapes spatial genome organization essential for gene expression control: lessons learned from the vitamin D receptor. PMID:35325193
Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. PMID:35269428
Base-resolution prediction of transcription factor binding signals by a deep learning framework. PMID:35263332
KLF15 cistromes reveal a hepatocyte pathway governing plasma corticosteroid transport and systemic inflammation. PMID:35263131
Coordinated Cross-Talk Between the Myc and Mlx Networks in Liver Regeneration and Neoplasia. PMID:35259493
CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants. PMID:35252945
Bone Marrow Stroma-Induced Transcriptome and Regulome Signatures of Multiple Myeloma. PMID:35205675
EZH2 Mediates Proliferation, Migration, and Invasion Promoted by Estradiol in Human Glioblastoma Cells. PMID:35197928
Tcf1 preprograms the mobilization of glycolysis in central memory CD8+ T cells during recall responses. PMID:35190717
Uncovering the mesendoderm gene regulatory network through multi-omic data integration. PMID:35172134
Biallelic mutations in cancer genomes reveal local mutational determinants. PMID:35145300
Aberrant somatic hypermutation of CCND1 generates non-coding drivers of mantle cell lymphomagenesis. PMID:35145272
Computational estimates of annular diameter reveal genetic determinants of mitral valve function and disease. PMID:35132965
TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer. PMID:35122059
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites. PMID:35115371
CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps. PMID:35100425
spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer-promoter interactions. PMID:35100401
Transcription factor regulation of eQTL activity across individuals and tissues. PMID:35100260
Identifying differential regulatory control of APOE ɛ4 on African versus European haplotypes as potential therapeutic targets. PMID:34978147
Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data. PMID:34953471
Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development. PMID:34942352
A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride. PMID:34900134
Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. PMID:34888502
Cell-type specialization is encoded by specific chromatin topologies. PMID:34789882
Explainable deep neural networks for novel viral genome prediction. PMID:34764607
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. PMID:34755879
ImmReg: the regulon atlas of immune-related pathways across cancer types. PMID:34755873
Comparative Analyses of Sperm DNA Methylomes Among Three Commercial Pig Breeds Reveal Vital Hypomethylated Regions Associated With Spermatogenesis and Embryonic Development. PMID:34691153
Global Histone H3 Lysine 4 Trimethylation (H3K4me3) Landscape Changes in Response to TGFβ. PMID:34671716
TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesis. PMID:34663818
Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells. PMID:34662402
The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. PMID:34650237
A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation. PMID:34649616
Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin. PMID:34635836
Bevacizumab-induced hypertension and proteinuria: a genome-wide study of more than 1000 patients. PMID:34616010
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data. PMID:34607350
SBSA: an online service for somatic binding sequence annotation. PMID:34606615
Systematic Evaluation of DNA Sequence Variations on in vivo Transcription Factor Binding Affinity. PMID:34567058
Tumor Necrosis Factor-alpha utilizes MAPK/NFκB pathways to induce cholesterol-25 hydroxylase for amplifying pro-inflammatory response via 25-hydroxycholesterol-integrin-FAK pathway. PMID:34551004
The transcription factor reservoir and chromatin landscape in activated plasmacytoid dendritic cells. PMID:34544361
Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. PMID:34524848
Chromatin-based, in cis and in trans regulatory rewiring underpins distinct oncogenic transcriptomes in multiple myeloma. PMID:34521827
Information content differentiates enhancers from silencers in mouse photoreceptors. PMID:34486522
YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation. PMID:34463254
Autosomal sex-associated co-methylated regions predict biological sex from DNA methylation. PMID:34403484
Filtering of Data-Driven Gene Regulatory Networks Using Drosophila melanogaster as a Case Study. PMID:34394179
Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus. PMID:34390653
Discovering differential genome sequence activity with interpretable and efficient deep learning. PMID:34370721
Loss of the MAF Transcription Factor in Laryngeal Squamous Cell Carcinoma. PMID:34356658
Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH. PMID:34326544
A Panel of rSNPs Demonstrating Allelic Asymmetry in Both ChIP-seq and RNA-seq Data and the Search for Their Phenotypic Outcomes through Analysis of DEGs. PMID:34298860
Meiotic recombination mirrors patterns of germline replication in mice and humans. PMID:34260899
EGR1 and RXRA transcription factors link TGF-β pathway and CCL2 expression in triple negative breast cancer cells. PMID:34239022
Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer. PMID:34215221
Regulatory SNPs: Altered Transcription Factor Binding Sites Implicated in Complex Traits and Diseases. PMID:34208629
Profiling DNA break sites and transcriptional changes in response to contextual fear learning. PMID:34197463
A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes. PMID:34193535
Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans. PMID:34159315
Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. PMID:34155196
Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas. PMID:34131149
Skin and gut imprinted helper T cell subsets exhibit distinct functional phenotypes in central nervous system autoimmunity. PMID:34099917
Plasma Membrane Calcium ATPase Regulates Stoichiometry of CD4+ T-Cell Compartments. PMID:34093590
Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment. PMID:34079046
Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer. PMID:34070697
A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta. PMID:34044884
Transcription Factor-Binding Site Identification and Enrichment Analysis. PMID:34033108
Use of scREAD to explore and analyze single-cell and single-nucleus RNA-seq data for Alzheimer's disease. PMID:34013209
Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes. PMID:34009325
Integrative methylome-transcriptome analysis unravels cancer cell vulnerabilities in infant MLL-rearranged B cell acute lymphoblastic leukemia. PMID:33983906
Landscape of allele-specific transcription factor binding in the human genome. PMID:33980847
Genome-wide histone acetylation analysis reveals altered transcriptional regulation in the Parkinson's disease brain. PMID:33947435
Bayesian Markov models improve the prediction of binding motifs beyond first order. PMID:33928244
Statistical mechanics meets single-cell biology. PMID:33875884
Deep neural networks identify sequence context features predictive of transcription factor binding. PMID:33796819
Epigenomic tensor predicts disease subtypes and reveals constrained tumor evolution. PMID:33789109
Auto-aggressive CXCR6+ CD8 T cells cause liver immune pathology in NASH. PMID:33762736
A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes. PMID:33753848
Fast decoding cell type-specific transcription factor binding landscape at single-nucleotide resolution. PMID:33741685
Single Cell RNA-Seq and Machine Learning Reveal Novel Subpopulations in Low-Grade Inflammatory Monocytes With Unique Regulatory Circuits. PMID:33708217
Transcriptional Profiling of STAT1 Gain-of-Function Reveals Common and Mutation-Specific Fingerprints. PMID:33679782
The glucocorticoid receptor recruits the COMPASS complex to regulate inflammatory transcription at macrophage enhancers. PMID:33567280
Regulatory genomic circuitry of human disease loci by integrative epigenomics. PMID:33536621
Locating transcription factor binding sites by fully convolutional neural network. PMID:33498086
Cell lineage-specific methylome and genome alterations in gout. PMID:33493135
Mitochondrial TSPO Deficiency Triggers Retrograde Signaling in MA-10 Mouse Tumor Leydig Cells. PMID:33383772
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. PMID:33352111
Genes associated with cognitive performance in the Morris water maze: an RNA-seq study. PMID:33328525
The MUC5B-associated variant rs35705950 resides within an enhancer subject to lineage- and disease-dependent epigenetic remodeling. PMID:33320836
Evidence of widespread, independent sequence signature for transcription factor cobinding. PMID:33303494
Single-cell lineage analysis reveals extensive multimodal transcriptional control during directed beta-cell differentiation. PMID:33257854
A map of cis-regulatory elements and 3D genome structures in zebrafish. PMID:33239788
GTRD: an integrated view of transcription regulation. PMID:33231677
Dedifferentiation and neuronal repression define familial Alzheimer's disease. PMID:33188013
Exploring functionally annotated transcriptional consensus regulatory elements with CONREL. PMID:33186463
Learning and interpreting the gene regulatory grammar in a deep learning framework. PMID:33137083
Meta-Analysis of Transcriptome Data Detected New Potential Players in Response to Dioxin Exposure in Humans. PMID:33113971
VARAdb: a comprehensive variation annotation database for human. PMID:33095866
Analyzing a putative enhancer of optic disc morphology. PMID:33092545
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
Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells. PMID:33057200
HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression. PMID:33021676
Long Noncoding RNA OIP5-AS1 Promotes Cell Apoptosis and Cataract Formation by Blocking POLG Expression Under Oxidative Stress. PMID:33006594
TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma. PMID:32925947
The Polygenic and Monogenic Basis of Blood Traits and Diseases. PMID:32888494
Multiomics dissection of molecular regulatory mechanisms underlying autoimmune-associated noncoding SNPs. PMID:32879140
hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets. PMID:32858223
ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. PMID:32848148
Asymmetric Conservation within Pairs of Co-Occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-Seq Data. PMID:32825662
Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss. PMID:32816922
Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons. PMID:32794569
Metabolic effects of air pollution exposure and reversibility. PMID:32780721
Integrative analyses of single-cell transcriptome and regulome using MAESTRO. PMID:32767996
ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants. PMID:32765587
Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. PMID:32735851
Global reference mapping of human transcription factor footprints. PMID:32728250
DNA methylation enables transposable element-driven genome expansion. PMID:32719115
The Meningioma Enhancer Landscape Delineates Novel Subgroups and Drives Druggable Dependencies. PMID:32703768
MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function. PMID:32657363
Systemic Investigation of Promoter-wide Methylome and Genome Variations in Gout. PMID:32630231
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma. PMID:32483191
A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors. PMID:32461370
IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq. PMID:32421805
KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs. PMID:32402252
Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study. PMID:32393327
Controlling gene activation by enhancers through a drug-inducible topological insulator. PMID:32369019
Epigenetic regulation of neuronal cell specification inferred with single cell "Omics" data. PMID:32368329
Deactivation of Glutaminolysis Sensitizes PIK3CA-Mutated Colorectal Cancer Cells to Aspirin-Induced Growth Inhibition. PMID:32365457
Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei. PMID:32365093
TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions. PMID:32324215
Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia. PMID:32303558
Sporadic activation of an oxidative stress-dependent NRF2-p53 signaling network in breast epithelial spheroids and premalignancies. PMID:32291314
Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension. PMID:32245974
The physical basis and practical consequences of biological promiscuity. PMID:32244231
Krüppel-like factor 3 (KLF3) suppresses NF-κB-driven inflammation in mice. PMID:32213596
Phosphorylated Lamin A/C in the Nuclear Interior Binds Active Enhancers Associated with Abnormal Transcription in Progeria. PMID:32208162
DNA methylation disruption reshapes the hematopoietic differentiation landscape. PMID:32203468
LogoJS: a Javascript package for creating sequence logos and embedding them in web applications. PMID:32181813
HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancer. PMID:32154941
Epigenetic modulation of AREL1 and increased HLA expression in brains of multiple system atrophy patients. PMID:32151281
Glycosylation of immunoglobulin G is regulated by a large network of genes pleiotropic with inflammatory diseases. PMID:32128391
Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations. PMID:32078798
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
Towards a comprehensive catalogue of validated and target-linked human enhancers. PMID:31988385
A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods. PMID:31969180
A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome. PMID:31956652
Rad51 paralogs and the risk of unselected breast cancer: A case-control study. PMID:31905201
Combinatorial interactions of the LEC1 transcription factor specify diverse developmental programs during soybean seed development. PMID:31892538
Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs. PMID:31856658
Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages. PMID:31792380
Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination. PMID:31777934
TFregulomeR reveals transcription factors' context-specific features and functions. PMID:31754708
A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. PMID:31750523
Improved linking of motifs to their TFs using domain information. PMID:31742324
What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants. PMID:31737053
JASPAR 2020: update of the open-access database of transcription factor binding profiles. PMID:31701148
NPInter v4.0: an integrated database of ncRNA interactions. PMID:31670377
Retrotransposons spread potential cis-regulatory elements during mammary gland evolution. PMID:31642473
Reconstruction of the Global Neural Crest Gene Regulatory Network In Vivo. PMID:31639368
Spliceosomal disruption of the non-canonical BAF complex in cancer. PMID:31597964
MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex. PMID:31561554
Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration. PMID:31560769
CGGBP1 regulates CTCF occupancy at repeats. PMID:31547883
A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics. PMID:31533246
Deep insights into the response of human cervical carcinoma cells to a new cyano enone-bearing triterpenoid soloxolone methyl: a transcriptome analysis. PMID:31523389
Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression. PMID:31519741
Reconstruction and Analysis of Gene Networks of Human Neurotransmitter Systems Reveal Genes with Contentious Manifestation for Anxiety, Depression, and Intellectual Disabilities. PMID:31514272
Deciphering epigenomic code for cell differentiation using deep learning. PMID:31510916
SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes. PMID:31477007
A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line. PMID:31363108
Roles of p53 Family Structure and Function in Non-Canonical Response Element Binding and Activation. PMID:31357595
Epigenomics and Single-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis. PMID:31345789
Benchmark and integration of resources for the estimation of human transcription factor activities. PMID:31340985
Identification of DNA motifs that regulate DNA methylation. PMID:31334813
Single Nucleotide Polymorphisms at a Distance from Aryl Hydrocarbon Receptor (AHR) Binding Sites Influence AHR Ligand-Dependent Gene Expression. PMID:31292129
Computer genomics research at the bioinformatics conference series in Novosibirsk. PMID:31291908
Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes. PMID:31283382
Unified single-cell analysis of testis gene regulation and pathology in five mouse strains. PMID:31237565
Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function. PMID:31221079
Genetic resistance to DEHP-induced transgenerational endocrine disruption. PMID:31181066
Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity. PMID:31175293
ChEA3: transcription factor enrichment analysis by orthogonal omics integration. PMID:31114921
QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. PMID:31114870
Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay. PMID:31106481
TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes. PMID:31045203
ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer. PMID:31000713
Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons. PMID:30970224
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data. PMID:30962623
Primary endothelial cell-specific regulation of hypoxia-inducible factor (HIF)-1 and HIF-2 and their target gene expression profiles during hypoxia. PMID:30917010
Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control. PMID:30858428
Epigenetic regulation of REX1 expression and chromatin binding specificity by HMGNs. PMID:30838422
Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. PMID:30696717
Tissue-Specific Trans Regulation of the Mouse Epigenome. PMID:30593494
Heterodimeric DNA motif synthesis and validations. PMID:30590725
The Identification and Interpretation of cis-Regulatory Noncoding Mutations in Cancer. PMID:30577431
Anchor: trans-cell type prediction of transcription factor binding sites. PMID:30567711
GTRD: a database on gene transcription regulation-2019 update. PMID:30445619
Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus. PMID:30444878
MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. PMID:30380113
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. PMID:30364927
Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data. PMID:30352610
Control of directionality of chromatin folding for the inter- and intra-domain contacts at the Tfap2c-Bmp7 locus. PMID:30213272
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. PMID:30204897
Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. PMID:30177862
A network of epigenomic and transcriptional cooperation encompassing an epigenomic master regulator in cancer. PMID:29977600
c-Myc is a novel Leishmania virulence factor by proxy that targets the host miRNA system and is essential for survival in human macrophages. PMID:29934305
The BaMM web server for de-novo motif discovery and regulatory sequence analysis. PMID:29846656
Molecular and Functional Sex Differences of Noradrenergic Neurons in the Mouse Locus Coeruleus. PMID:29791834
Differential Expression Profiling of Long Noncoding RNA and mRNA during Osteoblast Differentiation in Mouse. PMID:29765976
Detecting Differential Transcription Factor Activity from ATAC-Seq Data. PMID:29748466
PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix. PMID:29514181
Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation. PMID:29491135 -
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
PubMed citations: 111.
111 articles citing: HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
Predicting 3D chromatin interactions from DNA sequence using Deep Learning. PMID:35832620
The hypoxia-induced changes in miRNA-mRNA in RNA-induced silencing complexes and HIF-2 induced miRNAs in human endothelial cells. PMID:35713587
Disrupted myelination network in the cingulate cortex of Parkinson's disease. PMID:35394697
CDK7/12/13 inhibition targets an oscillating leukemia stem cell network and synergizes with venetoclax in acute myeloid leukemia. PMID:35253392
Bioinformatics pipeline to guide late-onset Alzheimer's disease (LOAD) post-GWAS studies: Prioritizing transcription regulatory variants within LOAD-associated regions. PMID:35229021
Polympact: exploring functional relations among common human genetic variants. PMID:35061909
Molecular Pathways Modulating Sensory Hair Cell Regeneration in Adult Mammalian Cochleae: Progress and Perspectives. PMID:35008497
Estrogen-Driven Changes in Immunoglobulin G Fc Glycosylation. PMID:34687016
Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics data. PMID:33837132
Multi-omics analysis of tumor angiogenesis characteristics and potential epigenetic regulation mechanisms in renal clear cell carcinoma. PMID:33761933
Characterizing RNA Pseudouridylation by Convolutional Neural Networks. PMID:33631424
Evolution of regulatory networks associated with traits under selection in cichlids. PMID:33419455
Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi's Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins. PMID:33193257
A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease. PMID:33138777
Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks. PMID:33006313
The Gene-Regulatory Footprint of Aging Highlights Conserved Central Regulators. PMID:32997995
Abnormal Activations of Super-Enhancers Enhance the Carcinogenicity in Lung Adenocarcinoma. PMID:32982443
Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites. PMID:32946763
Identification of dysregulated miRNAs-genes network in ovarian cancer: An integrative approach to uncover the molecular interactions and oncomechanisms. PMID:32886452
Leverage Large-Scale Biological Networks to Decipher the Genetic Basis of Human Diseases Using Machine Learning. PMID:32804369
TCF7L2 regulates postmitotic differentiation programmes and excitability patterns in the thalamus. PMID:32675279
Inherited variant in NFκB-1 promoter is associated with increased risk of IBD in an Algerian population and modulates SOX9 binding. PMID:32671985
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis. PMID:32014034
Towards a comprehensive catalogue of validated and target-linked human enhancers. PMID:31988385
A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV. PMID:31968263
Comparative and Functional Genomic Resource for Mechanistic Studies of Human Blood Pressure-Associated Single Nucleotide Polymorphisms. PMID:31902252
'One DB to rule them all'-the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs. PMID:31682269
Sequence and chromatin determinants of transcription factor binding and the establishment of cell type-specific binding patterns. PMID:31639474
A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics. PMID:31533246
Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions. PMID:31495563
Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays. PMID:31481462
Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response. PMID:31362726
A herpesvirus transactivator and cellular POU proteins extensively regulate DNA binding of the host Notch signaling protein RBP-Jκ to the virus genome. PMID:31308175
Uncovering a mitochondrial unfolded protein response in corals and its role in adapting to a changing world. PMID:31238849
Finding de novo methylated DNA motifs. PMID:30726880
Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. PMID:30696717
Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. PMID:30664630
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. PMID:30612741
Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. PMID:30555922
Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions. PMID:30455182
OncoBase: a platform for decoding regulatory somatic mutations in human cancers. PMID:30445567
Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors. PMID:30359306
Cell-type-specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes. PMID:30333196
Positional integration of lung adenocarcinoma susceptibility loci with primary human alveolar epithelial cell epigenomes. PMID:30212242
Enhancer reprogramming in mammalian genomes. PMID:30200877
Functional characterization of enhancer evolution in the primate lineage. PMID:30045748
VHL inactivation without hypoxia is sufficient to achieve genome hypermethylation. PMID:30006568
Early metazoan cell type diversity and the evolution of multicellular gene regulation. PMID:29942020
Detecting Differential Transcription Factor Activity from ATAC-Seq Data. PMID:29748466
Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis. PMID:29708547
TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets. PMID:29621972
A novel method for improved accuracy of transcription factor binding site prediction. PMID:29617876
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. PMID:29617668
Enhancer RNA profiling predicts transcription factor activity. PMID:29449408
Network analysis of SRC-1 reveals a novel transcription factor hub which regulates endocrine resistant breast cancer. PMID:29367763
THiCweed: fast, sensitive detection of sequence features by clustering big datasets. PMID:29267972
Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins. PMID:29146583
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. PMID:29140464
An improved compound Poisson model for the number of motif hits in DNA sequences. PMID:28961747
Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines. PMID:28869592
Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. PMID:28691125
Inherited determinants of early recurrent somatic mutations in prostate cancer. PMID:28663546
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PMID:28257516
Genome-wide association analysis implicates dysregulation of immunity genes in chronic lymphocytic leukaemia. PMID:28165464
Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility. PMID:28118358
Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci. PMID:28108556
SDHD Promoter Mutations Ablate GABP Transcription Factor Binding in Melanoma. PMID:28108517
Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer. PMID:28077088
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
Associations of the calcium-sensing receptor gene CASR rs7652589 SNP with nephrolithiasis and secondary hyperparathyroidism in haemodialysis patients. PMID:27739473
Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate. PMID:27710791
Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms. PMID:27694855
Clustered somatic mutations are frequent in transcription factor binding motifs within proximal promoter regions in melanoma and other cutaneous malignancies. PMID:27611953
Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer. PMID:27571262
Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder. PMID:27479844
Genome-wide analysis of HIF-2α chromatin binding sites under normoxia in human bronchial epithelial cells (BEAS-2B) suggests its diverse functions. PMID:27373565
Negative selection maintains transcription factor binding motifs in human cancer. PMID:27356864
Allelic Imbalance in Regulation of ANRIL through Chromatin Interaction at 9p21 Endometriosis Risk Locus. PMID:27055116
Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. PMID:26941778
Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer. PMID:26769127
Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line. PMID:26635867
Progress and challenges in bioinformatics approaches for enhancer identification. PMID:26634919
Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network. PMID:26604129
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. PMID:26586801
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
Common variants at the CHEK2 gene locus and risk of epithelial ovarian cancer. PMID:26424751
DENdb: database of integrated human enhancers. PMID:26342387
Reliable scaling of position weight matrices for binding strength comparisons between transcription factors. PMID:26289072
motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. PMID:26272984
Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal. PMID:26267829
EpiFactors: a comprehensive database of human epigenetic factors and complexes. PMID:26153137
Insights into the Transcriptional Architecture of Behavioral Plasticity in the Honey Bee Apis mellifera. PMID:26073445
Adaptation of peroxisome proliferator-activated receptor alpha to hibernation in bats. PMID:25980933
Optimally choosing PWM motif databases and sequence scanning approaches based on ChIP-seq data. PMID:25927199
Identification of a Novel Mucin Gene HCG22 Associated With Steroid-Induced Ocular Hypertension. PMID:25813999
Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci. PMID:25804953
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples. PMID:25725063
Analysis of pattern overlaps and exact computation of P-values of pattern occurrences numbers: case of Hidden Markov Models. PMID:25648087
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. PMID:25505144
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes. PMID:25428367
DEEP: a general computational framework for predicting enhancers. PMID:25378307
TFClass: a classification of human transcription factors and their rodent orthologs. PMID:25361979
Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes. PMID:25275320
Comparative evaluation of DNase-seq footprint identification strategies. PMID:25177346
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. PMID:24927817
On the identification of potential regulatory variants within genome wide association candidate SNP sets. PMID:24920305
Effects of cytosine methylation on transcription factor binding sites. PMID:24669864
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data. PMID:24472686
Jaccard index based similarity measure to compare transcription factor binding site models. PMID:24074225
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983 -
Deep and wide digging for binding motifs in ChIP-Seq data
PubMed citations: 75.
75 articles citing: Deep and wide digging for binding motifs in ChIP-Seq data
Interaction between transcribing RNA polymerase and topoisomerase I prevents R-loop formation in E. coli. PMID:35927234
Bayesian Markov models improve the prediction of binding motifs beyond first order. PMID:33928244
The PhoPQ Two-Component System Is the Major Regulator of Cell Surface Properties, Stress Responses and Plant-Derived Substrate Utilisation During Development of Pectobacterium versatile-Host Plant Pathosystems. PMID:33519782
Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-Seq) Analysis in Ewing Sarcoma. PMID:33326109
A Clustering Approach for Motif Discovery in ChIP-Seq Dataset. PMID:33267515
Set cover-based methods for motif selection. PMID:31665223
Population size estimation for quality control of ChIP-Seq datasets. PMID:31465497
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework. PMID:31372637
Dicyemida and Orthonectida: Two Stories of Body Plan Simplification. PMID:31178892
Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs. PMID:31098334
ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery. PMID:31070745
RECAP reveals the true statistical significance of ChIP-seq peak calls. PMID:30824903
Performance evaluation for MOTIFSIM. PMID:30574025
Anchor: trans-cell type prediction of transcription factor binding sites. PMID:30567711
A map of direct TF-DNA interactions in the human genome. PMID:30517703
Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome. PMID:30517674
MODSIDE: a motif discovery pipeline and similarity detector. PMID:30340511
VHL inactivation without hypoxia is sufficient to achieve genome hypermethylation. PMID:30006568
A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction. PMID:29654070
Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets. PMID:29385521
THiCweed: fast, sensitive detection of sequence features by clustering big datasets. PMID:29267972
IRF8-dependent molecular complexes control the Th9 transcriptional program. PMID:29233972
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. PMID:29140464
RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. PMID:28591841
Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. PMID:28526842
Transcription factor-DNA binding: beyond binding site motifs. PMID:28359978
Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility. PMID:28334916
In silico evolution of the Drosophila gap gene regulatory sequence under elevated mutational pressure. PMID:28251865
Unrealistic phylogenetic trees may improve phylogenetic footprinting. PMID:28130227
Evaluating tools for transcription factor binding site prediction. PMID:27806697
Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila. PMID:27137890
Searching the Human Genome for Snail and Slug With DNA@Home. PMID:26998498
Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. PMID:26941778
Analysis of functional importance of binding sites in the Drosophila gap gene network model. PMID:26694511
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. PMID:26586801
DiffLogo: a comparative visualization of sequence motifs. PMID:26577052
A Fast Cluster Motif Finding Algorithm for ChIP-Seq Data Sets. PMID:26236718
c-Myb Binding Sites in Haematopoietic Chromatin Landscapes. PMID:26208222
MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures. PMID:26099518
BolA is a transcriptional switch that turns off motility and turns on biofilm development. PMID:25691594
Sequence-based model of gap gene regulatory network. PMID:25564104
Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome. PMID:25563792
Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs. PMID:25505144
De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets. PMID:25442502
Multiple novel promoter-architectures revealed by decoding the hidden heterogeneity within the genome. PMID:25326324
Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. PMID:25180570
The NF-κB genomic landscape in lymphoblastoid B cells. PMID:25159142
Transcription factor regulation and chromosome dynamics during pseudohyphal growth. PMID:25009286
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. PMID:24927817
Motif-based analysis of large nucleotide data sets using MEME-ChIP. PMID:24853928
A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data. PMID:24555784
A new exhaustive method and strategy for finding motifs in ChIP-enriched regions. PMID:24475069
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data. PMID:24472686
Discriminative motif optimization based on perceptron training. PMID:24369152
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data. PMID:24322294
Practical guidelines for the comprehensive analysis of ChIP-seq data. PMID:24244136
A general approach for discriminative de novo motif discovery from high-throughput data. PMID:24057214
Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease. PMID:23849224
TherMos: Estimating protein-DNA binding energies from in vivo binding profiles. PMID:23595148
Evaluation of methods for modeling transcription factor sequence specificity. PMID:23354101
MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis. PMID:23323883
A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs. PMID:23181585
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. PMID:23175603
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
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PMID:22912568
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. PMID:22836136
Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia. PMID:22790984
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era. PMID:22517426
A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. PMID:22228832
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. PMID:22156162
Tree-based position weight matrix approach to model transcription factor binding site profiles. PMID:21912677
GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge. PMID:21513505
An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq. PMID:21358819
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. PMID:21183585 -
From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites
PubMed citations: 29.
29 articles citing: From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites
A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC. PMID:34049974
Bayesian Markov models improve the prediction of binding motifs beyond first order. PMID:33928244
Mechanism and functional role of the interaction between CP190 and the architectural protein Pita in Drosophila melanogaster. PMID:33752739
Deciphering GRINA/Lifeguard1: Nuclear Location, Ca2+ Homeostasis and Vesicle Transport. PMID:31426446
ChIPulate: A comprehensive ChIP-seq simulation pipeline. PMID:30897079
A map of direct TF-DNA interactions in the human genome. PMID:30517703
Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production. PMID:30338257
Disentangling transcription factor binding site complexity. PMID:30085218
The BaMM web server for de-novo motif discovery and regulatory sequence analysis. PMID:29846656
THiCweed: fast, sensitive detection of sequence features by clustering big datasets. PMID:29267972
IRF8-dependent molecular complexes control the Th9 transcriptional program. PMID:29233972
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. PMID:29140464
Noncoding Variants Functional Prioritization Methods Based on Predicted Regulatory Factor Binding Sites. PMID:29081688
Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. PMID:28526842
Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility. PMID:28334916
Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies. PMID:28249564
The single nucleotide variant rs12722489 determines differential estrogen receptor binding and enhancer properties of an IL2RA intronic region. PMID:28234966
Evaluating tools for transcription factor binding site prediction. PMID:27806697
Nucleotide Interdependency in Transcription Factor Binding Sites in the Drosophila Genome. PMID:27330274
Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. PMID:27288444
Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions in Drosophila. PMID:27137890
Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. PMID:26941778
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. PMID:26586801
Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal. PMID:26267829
Varying levels of complexity in transcription factor binding motifs. PMID:26116565
MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding. PMID:25637281
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data. PMID:24472686
Predicting tissue specific transcription factor binding sites. PMID:24238150
A general approach for discriminative de novo motif discovery from high-throughput data. PMID:24057214 -
Jaccard index based similarity measure to compare transcription factor binding site models
PubMed citations: 19.
19 articles citing: Jaccard index based similarity measure to compare transcription factor binding site models
3DCoop: An approach for computational inference of cell-type-specific transcriptional regulators cooperation in 3D chromatin. PMID:35600920
Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. PMID:34888502
RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery. PMID:34841226
Deep learning classification of lipid droplets in quantitative phase images. PMID:33819277
Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology. PMID:33575595
Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study. PMID:32393327
MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex. PMID:31561554
Protease Activity Profiling of Snake Venoms Using High-Throughput Peptide Screening. PMID:30893860
Vertical disc tilt and features of the optic nerve head anatomy are related to visual field defect in myopic eyes. PMID:30837506
Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming. PMID:30517869
Subtle left-right asymmetry of gene expression profiles in embryonic and foetal human brains. PMID:30181561
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data. PMID:29800452
GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits. PMID:29771388
A novel method for improved accuracy of transcription factor binding site prediction. PMID:29617876
Modelling the evolution of transcription factor binding preferences in complex eukaryotes. PMID:28790414
RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. PMID:28591841
Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer. PMID:28077088
Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. PMID:26941778
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. PMID:26586801
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chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
curated information
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
transcription factor
metasource: Fairsharing.org
version: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
dna binding sites
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:29.851370
chip-seq
metasource: bio.tools
version: extracted_at: 2022-11-04T11:23:29.851370
Tags
More detailed information about this field from each metasource.
chromatin immunoprecipitation - dna sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
curated information
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
transcription factor
metasource: Fairsharing.orgversion: FAIRsharing.org: HOCOMOCO; HOmo sapiens transcription factor COmprehensive MOdel COllection; DOI: https://doi.org/10.25504/FAIRsharing.c1bjep; Last edited: April 26, 2021, 8:22 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
nucleotide sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
transcriptional regulator sites and transcription factors
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
dna binding sites
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:29.851370
chip-seq
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:23:29.851370
chromatin immunoprecipitation - dna sequencing transcription nucleic acid sequence transcription dna binding sites chip-seq
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