ArticleNucleic acids research2019
GTRD: a database on gene transcription regulation-2019 update.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 173 papers, 1 of them a synthesis that pooled it.
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Who cites it
173 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Functional Gene Expression Differentiation of the Notch Signaling Pathway in Female Reproductive Tract Tissues-A Comprehensive Review With Analysis.Frontiers in cell and developmental biology · 2020Pooled it
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- PGC-1α pathway dysregulation disrupts myofiber specification in a mouse model of SBMA.JCI insight · 2026Article
- Review
- Actinobacteria TFDB: An integrated view of transcription factors in Actinobacteria.Engineering microbiology · 2026Article
- Plecstatin inhibits hepatocellular carcinoma tumorigenesis and invasion through cytolinker plectin.Molecular oncology · 2026Article
- Integrative Analyses Identify a cGAS-STING Pathway-Driven Signature With Context-Dependent Roles in Systemic Lupus Erythematosus.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Dynamic changes in chromatin accessibility reveal the role of NF-Y targeting AURKB in mediating cell cycle during asynchronous oogenesis in the Chinese Alligator (Alligator sinensis).Frontiers in zoology · 2026Article
- Multi-modal circulating cell-free DNA profiling to predict response to docetaxel in metastatic castration-resistant prostate cancer.NPJ precision oncology · 2026Article
- Integrative molecular analyses of lineage identity and morphology in aggressive variant prostate cancer.NPJ precision oncology · 2026Article
- Transcriptional repression of TGFB2-AS1 by GATA6 drives triple-negative breast cancer metastasis.Cellular oncology (Dordrecht, Netherlands) · 2026Article
- TET1 deficiency amplifies macrophage inflammatory signaling associated with Crohn's disease.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- Heat shock factor-1 alleviates ER-stress in Caenorhabditis elegans.Scientific reports · 2026Article
- Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium.bioRxiv : the preprint server for biology · 2026Article
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- Molecular decoupling of lineage identity and morphology in aggressive variant prostate cancer.medRxiv : the preprint server for health sciences · 2026Article
- Exploring potential transcription factors and their regulatory relationships based on asymmetric covariance natural vector encoding method and machine learning algorithms.Briefings in bioinformatics · 2026Article
- SEdb 3.0: a comprehensive super-enhancer database across multiple species.Nucleic acids research · 2026Article
- Transcriptional activation of ALOX5 by c-Myc drives malignant progression and M2 macrophage polarization in clear cell renal cell carcinoma.American journal of cancer research · 2026Article
- FAM111B promotes prostate cancer progression by inhibiting apoptosis via ATF3 suppression and MAPK pathway activation: a novel biomarker and therapeutic target.Cancer cell international · 2025Article
113 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The current version of the Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org) contains information about: (i) transcription factor binding sites (TFBSs) and transcription coactivators identified by ChIP-seq experiments for Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Arabidopsis thaliana; (ii) regions of open chromatin and TFBSs (DNase footprints) identified by DNase-seq; (iii) unmappable regions where TFBSs cannot be identified due to repeats; (iv) potential TFBSs for both human and mouse using position weight matrices from the HOCOMOCO database. Raw ChIP-seq and DNase-seq data were obtained from ENCODE and SRA, and uniformly processed. ChIP-seq peaks were called using four different methods: MACS, SISSRs, GEM and PICS. Moreover, peaks for the same factor and peak calling method, albeit using different experiment conditions (cell line, treatment, etc.), were merged into clusters. To reduce noise, such clusters for different peak calling methods were merged into meta-clusters; these were considered to be non-redundant TFBS sets. Moreover, extended quality control was applied to all ChIP-seq data. Web interface to access GTRD was developed using the BioUML platform. It provides browsing and displaying information, advanced search possibilities and an integrated genome browser.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.