Gene Transcription Regulation Database

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Gene Transcription Regulation Database

metasource: Fairsharing.org
version: None

---

GTRD

metasource: Fairsharing.org
version: None

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

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Other names: GTRD

Gene Transcription Regulation Database (GTRD) is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse.

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Publications

More detailed information about this field from each metasource. ×

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments
PMID: 27924024

metasource: Fairsharing.org
version: None

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GTRD: a database on gene transcription regulation-2019 update
PMID: 30445619

metasource: Fairsharing.org
version: None

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http://dx.doi.org/10.1093/nar/gky1128

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

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• GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments PubMed citations: 92.

  92 articles citing: GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

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  Upregulation of Thioredoxin Reductase 1 Expression by Flavan-3-Ols Protects Human Kidney Proximal Tubular Cells from Hypoxia-Induced Cell Death. PMID:35883890

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  E2F4 may be a core transcription factor in the lncRNA-TF regulatory network in cervical cancer. PMID:35262965

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  TRmir: A Comprehensive Resource for Human Transcriptional Regulatory Information of MiRNAs. PMID:35186035

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  Inferring protein expression changes from mRNA in Alzheimer's dementia using deep neural networks. PMID:35115553

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  Deep learning tackles single-cell analysis-a survey of deep learning for scRNA-seq analysis. PMID:34929734

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  Decoding the effects of synonymous variants. PMID:34850938

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  Physical exercise shapes the mouse brain epigenome. PMID:34801767

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  proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. PMID:34791440

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  Superenhancer-transcription factor regulatory network in malignant tumors. PMID:34722892

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  MYC Levels Regulate Metastatic Heterogeneity in Pancreatic Adenocarcinoma. PMID:34551968

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  Mechanisms of Binding Specificity among bHLH Transcription Factors. PMID:34502060

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  DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data. PMID:34424948

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  Meiotic recombination mirrors patterns of germline replication in mice and humans. PMID:34260899

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  Integrative methylome-transcriptome analysis unravels cancer cell vulnerabilities in infant MLL-rearranged B cell acute lymphoblastic leukemia. PMID:33983906

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  Deep learning of gene relationships from single cell time-course expression data. PMID:33876191

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  In vitro and in silico assessment of the effect of WWOX expression on invasiveness pathways associated with AP-2 transcription factors in bladder cancer. PMID:33691672

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  Evolution of regulatory networks associated with traits under selection in cichlids. PMID:33419455

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  Functional Gene Expression Differentiation of the Notch Signaling Pathway in Female Reproductive Tract Tissues-A Comprehensive Review With Analysis. PMID:33384996

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  Variable interplay of UV-induced DNA damage and repair at transcription factor binding sites. PMID:33347579

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  Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. PMID:33347457

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  Transcriptional network modulated by the prognostic signature transcription factors and their long noncoding RNA partners in primary prostate cancer. PMID:33279858

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  Lung squamous cell carcinoma and lung adenocarcinoma differential gene expression regulation through pathways of Notch, Hedgehog, Wnt, and ErbB signalling. PMID:33273537

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  GTRD: an integrated view of transcription regulation. PMID:33231677

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  Functional genomics of AP-2α and AP-2γ in cancers: in silico study. PMID:33213447

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  Comprehensive mapping of the human cytokine gene regulatory network. PMID:33179750

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  Bioinformatic characterization of angiotensin-converting enzyme 2, the entry receptor for SARS-CoV-2. PMID:33112891

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  A systems genomics approach to uncover the molecular properties of cancer genes. PMID:33110144

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  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

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  LncSEA: a platform for long non-coding RNA related sets and enrichment analysis. PMID:33045741

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  LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1. PMID:32863950

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  Beyond Trees: Regulons and Regulatory Motif Characterization. PMID:32854400

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  m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. PMID:32821938

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  Deep learning decodes the principles of differential gene expression. PMID:32671330

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  Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver. PMID:32407006

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  Empowering Retinal Gene Therapy with a Specific Promoter for Human Rod and Cone ON-Bipolar Cells. PMID:32258214

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  Genome-wide association identifies seven loci for pelvic organ prolapse in Iceland and the UK Biobank. PMID:32184442

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  A paracrine activin A-mDia2 axis promotes squamous carcinogenesis via fibroblast reprogramming. PMID:32150356

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  Sexual dimorphism in atrophic effects of topical glucocorticoids is driven by differential regulation of atrophogene REDD1 in male and female skin. PMID:32064044

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  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

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  ChIPSummitDB: a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them. PMID:31942977

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  Discovering master regulators in hepatocellular carcinoma: one novel MR, SEC14L2 inhibits cancer cells. PMID:31851620

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  Deep learning for inferring gene relationships from single-cell expression data. PMID:31822622

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  What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants. PMID:31737053

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  An integrated epigenome and transcriptome analysis identifies PAX2 as a master regulator of drug resistance in high grade pancreatic ductal adenocarcinoma. PMID:31622355

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  Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection. PMID:31604930

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  KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors. PMID:31598675

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  Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines. PMID:31537905

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  Population size estimation for quality control of ChIP-Seq datasets. PMID:31465497

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  Genotoxic stress-triggered β-catenin/JDP2/PRMT5 complex facilitates reestablishing glutathione homeostasis. PMID:31434880

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  PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543

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  Impact of vitamin D and vitamin D receptor TaqI polymorphism in primary human myoblasts. PMID:31252402

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  Transcriptomic Network Interactions in Human Skin Treated with Topical Glucocorticoid Clobetasol Propionate. PMID:31247200

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  Developmental dynamics of lncRNAs across mammalian organs and species. PMID:31243368

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  A Novel Set of WNT Pathway Effectors as a Predictive Marker of Uterine Corpus Endometrial Carcinoma-Study Based on Weighted Co-expression Matrices. PMID:31134156

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  BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. PMID:31131402

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  HCP5 is a SMAD3-responsive long non-coding RNA that promotes lung adenocarcinoma metastasis via miR-203/SNAI axis. PMID:31131047

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  Gene expression and DNA methylation as mechanisms of disturbed metabolism in offspring after exposure to a prenatal HF diet. PMID:31064776

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  SEanalysis: a web tool for super-enhancer associated regulatory analysis. PMID:31028388

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  PI3K inhibitors protect against glucocorticoid-induced skin atrophy. PMID:30737086

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  CpG traffic lights are markers of regulatory regions in human genome. PMID:30709331

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  EnhancerDB: a resource of transcriptional regulation in the context of enhancers. PMID:30689845

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  A map of direct TF-DNA interactions in the human genome. PMID:30517703

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  ERRα promotes breast cancer cell dissemination to bone by increasing RANK expression in primary breast tumors. PMID:30478447

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  Characterization of Transcriptome Transition Associates Long Noncoding RNAs with Glioma Progression. PMID:30472640

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  GTRD: a database on gene transcription regulation-2019 update. PMID:30445619

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  TFmapper: A Tool for Searching Putative Factors Regulating Gene Expression Using ChIP-seq Data. PMID:30416387

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  ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data. PMID:30413482

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  PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277

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  MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles. PMID:30380113

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  TransmiR v2.0: an updated transcription factor-microRNA regulation database. PMID:30371815

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  Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data. PMID:30352610

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  An Evolutionarily Conserved Mesodermal Enhancer in Vertebrate Zic3. PMID:30297839

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  Detecting genome-wide directional effects of transcription factor binding on polygenic disease risk. PMID:30177862

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  Endolysosomal degradation of Tau and its role in glucocorticoid-driven hippocampal malfunction. PMID:30166454

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  Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline. PMID:30140277

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  Functional interplay between c-Myc and Max in B lymphocyte differentiation. PMID:30126925

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  Disentangling transcription factor binding site complexity. PMID:30085218

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  Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver. PMID:30069000

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  Regulatory variants: from detection to predicting impact. PMID:29893792

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  snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions. PMID:29878048

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  The BaMM web server for de-novo motif discovery and regulatory sequence analysis. PMID:29846656

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  Rapid and Efficient FISH using Pre-Labeled Oligomer Probes. PMID:29844509

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  Core signaling pathways in ovarian cancer stem cell revealed by integrative analysis of multi-marker genomics data. PMID:29723215

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  Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis. PMID:29708547

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  Rapamycin Modulates Glucocorticoid Receptor Function, Blocks Atrophogene REDD1, and Protects Skin from Steroid Atrophy. PMID:29596905

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  Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3. PMID:29504919

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  The Role of Indoleamine-2,3-Dioxygenase in Cancer Development, Diagnostics, and Therapy. PMID:29445380

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  Genetic variants in ADAMTS13 as well as smoking are major determinants of plasma ADAMTS13 levels. PMID:29296746

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  RUNX1 promote invasiveness in pancreatic ductal adenocarcinoma through regulating miR-93. PMID:29245924

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  HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. PMID:29140464

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  ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments. PMID:29126285

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  EpiDenovo: a platform for linking regulatory de novo mutations to developmental epigenetics and diseases. PMID:29040751
• GTRD: a database on gene transcription regulation-2019 update PubMed citations: 80.

  80 articles citing: GTRD: a database on gene transcription regulation-2019 update

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  Lineage-specific rearrangement of chromatin loops and epigenomic features during adipocytes and osteoblasts commitment. PMID:35906483

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  Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration in mice. PMID:35906210

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  Altered Transcriptional Regulation of Glycolysis in Circulating CD8+ T Cells of Rheumatoid Arthritis Patients. PMID:35886000

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  Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets. PMID:35672799

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  A hominoid-specific endogenous retrovirus may have rewired the gene regulatory network shared between primordial germ cells and naïve pluripotent cells. PMID:35551519

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  Type I interferon transcriptional network regulates expression of coinhibitory receptors in human T cells. PMID:35301508

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  Identification of transcriptional regulatory network associated with response of host epithelial cells to SARS-CoV-2. PMID:34907210

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  Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. PMID:34888502

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  First DNA Sequencing in Beninese Indigenous Cattle Breeds Captures New Milk Protein Variants. PMID:34828308

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  Inflammatory cytokine-regulated tRNA-derived fragment tRF-21 suppresses pancreatic ductal adenocarcinoma progression. PMID:34779408

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  Kynurenine derivative 3-HAA is an agonist ligand for transcription factor YY1. PMID:34563230

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  MYC Levels Regulate Metastatic Heterogeneity in Pancreatic Adenocarcinoma. PMID:34551968

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  Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. PMID:34454581

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  Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program. PMID:34446064

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  A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis. PMID:34367349

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  ACE2 protein expression within isogenic cell lines is heterogeneous and associated with distinct transcriptomes. PMID:34354120

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  Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia. PMID:34301992

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  WWOX Loses the Ability to Regulate Oncogenic AP-2γ and Synergizes with Tumor Suppressor AP-2α in High-Grade Bladder Cancer. PMID:34204827

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  A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes. PMID:34193535

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  UniBind: maps of high-confidence direct TF-DNA interactions across nine species. PMID:34174819

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  Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells. PMID:34127967

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  The Cyclin-Dependent Kinase 8 (CDK8) Inhibitor DCA Promotes a Tolerogenic Chemical Immunophenotype in CD4+ T Cells via a Novel CDK8-GATA3-FOXP3 Pathway. PMID:34124936

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  Transcription Factors BARX1 and DLX4 Contribute to Progression of Clear Cell Renal Cell Carcinoma via Promoting Proliferation and Epithelial-Mesenchymal Transition. PMID:34124141

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  Calycosin inhibits breast cancer cell migration and invasion by suppressing EMT via BATF/TGF-β1. PMID:34096887

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  Widespread Exaptation of L1 Transposons for Transcription Factor Binding in Breast Cancer. PMID:34070697

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  G-quadruplex structural variations in human genome associated with single-nucleotide variations and their impact on gene activity. PMID:34001600

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  OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. PMID:33999180

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  Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer. PMID:33987034

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  Landscape of allele-specific transcription factor binding in the human genome. PMID:33980847

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  Luminal A Breast Cancer Co-expression Network: Structural and Functional Alterations. PMID:33959148

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  Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. PMID:33850167

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  A novel CD209 polymorphism is associated with rheumatoid arthritis patients in Taiwan. PMID:33792986

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  A computer-guided design tool to increase the efficiency of cellular conversions. PMID:33712564

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  In vitro and in silico assessment of the effect of WWOX expression on invasiveness pathways associated with AP-2 transcription factors in bladder cancer. PMID:33691672

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  Notch Signaling Pathway in Cancer-Review with Bioinformatic Analysis. PMID:33673145

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  Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells. PMID:33647016

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  Benchmarking network-based gene prioritization methods for cerebral small vessel disease. PMID:33634312

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  A gene-environment-induced epigenetic program initiates tumorigenesis. PMID:33536616

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  TCF7 knockdown inhibits the imatinib resistance of chronic myeloid leukemia K562/G01 cells by neutralizing the Wnt/β‑catenin/TCF7/ABC transporter signaling axis. PMID:33416164

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  Functional Gene Expression Differentiation of the Notch Signaling Pathway in Female Reproductive Tract Tissues-A Comprehensive Review With Analysis. PMID:33384996

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  Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. PMID:33347457

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  Distinct Effects of Inflammation on Cytochrome P450 Regulation and Drug Metabolism: Lessons from Experimental Models and a Potential Role for Pharmacogenetics. PMID:33339226

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  Role of IRE1α in podocyte proteostasis and mitochondrial health. PMID:33298866

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  Lung squamous cell carcinoma and lung adenocarcinoma differential gene expression regulation through pathways of Notch, Hedgehog, Wnt, and ErbB signalling. PMID:33273537

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  GTRD: an integrated view of transcription regulation. PMID:33231677

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  LincSNP 3.0: an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements. PMID:33219661

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  Functional genomics of AP-2α and AP-2γ in cancers: in silico study. PMID:33213447

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  A Targeted Bioinformatics Assessment of Adrenocortical Carcinoma Reveals Prognostic Implications of GABA System Gene Expression. PMID:33187258

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  Genomic Analysis of Vascular Invasion in HCC Reveals Molecular Drivers and Predictive Biomarkers. PMID:33140851

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  Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells. PMID:33140047

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  A holistic view of mouse enhancer architectures reveals analogous pleiotropic effects and correlation with human disease. PMID:33138777

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  ATACdb: a comprehensive human chromatin accessibility database. PMID:33125076

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  VARAdb: a comprehensive variation annotation database for human. PMID:33095866

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  SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity. PMID:33075803

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  Expression Profiles of Long Non-coding RNA and Messenger RNA in Human Traumatic Brain Injury. PMID:32919233

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  Phenotypes from cell-free DNA. PMID:32873154

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  Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference. PMID:32859263

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  Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation. PMID:32741307

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  Overexpression of HOXA10 is associated with unfavorable prognosis of acute myeloid leukemia. PMID:32571260

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  Upregulation of Mlxipl induced by cJun in the spinal dorsal horn after peripheral nerve injury counteracts mechanical allodynia by inhibiting neuroinflammation. PMID:32518215

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  AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse. PMID:32406920

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  The gene for the lysosomal protein LAMP3 is a direct target of the transcription factor ATF4. PMID:32312748

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  eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research. PMID:32275707

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  Empowering Retinal Gene Therapy with a Specific Promoter for Human Rod and Cone ON-Bipolar Cells. PMID:32258214

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  BedSect: An Integrated Web Server Application to Perform Intersection, Visualization, and Functional Annotation of Genomic Regions From Multiple Datasets. PMID:32117432

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  A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072

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  Gene Prioritization through Consensus Strategy, Enrichment Methodologies Analysis, and Networking for Osteosarcoma Pathogenesis. PMID:32033398

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  MYC and Twist1 cooperate to drive metastasis by eliciting crosstalk between cancer and innate immunity. PMID:31933479

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  TFregulomeR reveals transcription factors' context-specific features and functions. PMID:31754708

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  A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package. PMID:31750523

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  What Do Neighbors Tell About You: The Local Context of Cis-Regulatory Modules Complicates Prediction of Regulatory Variants. PMID:31737053

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  JASPAR 2020: update of the open-access database of transcription factor binding profiles. PMID:31701148

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  Macrophage metabolic reprogramming aggravates aortic dissection through the HIF1α-ADAM17 pathway✰. PMID:31640947

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  Sox2 promotes expression of the ST6Gal-I glycosyltransferase in ovarian cancer cells. PMID:31610800

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  Population size estimation for quality control of ChIP-Seq datasets. PMID:31465497

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  Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon-Intron Split Analysis (EISA). PMID:31372646

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  Identification of DNA motifs that regulate DNA methylation. PMID:31334813

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  BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. PMID:31131402

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  The TP53 Apoptotic Network Is a Primary Mediator of Resistance to BCL2 Inhibition in AML Cells. PMID:31048320

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  The Dual-Specificity Phosphatase 10 (DUSP10): Its Role in Cancer, Inflammation, and Immunity. PMID:30939861
• http://dx.doi.org/10.1093/nar/gky1128

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Tags

More detailed information about this field from each metasource. ×

binding site

metasource: Fairsharing.org
version: None

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chromatin immunoprecipitation - dna sequencing

metasource: Fairsharing.org
version: None

---

gene

metasource: Fairsharing.org
version: None

---

transcript

metasource: Fairsharing.org
version: None

---

transcription factor

metasource: Fairsharing.org
version: None

---

transcription factor binding site prediction

metasource: Fairsharing.org
version: None

---

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

Close

binding site chromatin immunoprecipitation - dna sequencing gene transcript transcription transcription factor binding site prediction nucleic acid sequence transcription