Gene Transcription Regulation Database
The most complete collection of uniformly processed ChIP-seq data to identify transcription factor binding sites for human and mouse. Convenient web interface with advanced search, browsing and genome browser based on the BioUML platform. For support or any questions contact firstname.lastname@example.org
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How it was constructed?
ChIP-seq experiment information and raw data were collected from publically available sources. Sequenced reads were aligned using Bowtie2 and ChIP-seq peaks were called using 4 different methods. Peaks were merged into clusters and metaclusters to produce non-redundant set of transcription factor binding sites.Learn more »
- 3075 new 8828 ChIP-seq experiments
- 171 new 713 Transcription factors
- 51% new 372 107 532 423 ChIP-seq reads
- 39% new 239 502 628 829 Reads aligned
- 56% new 659 388 760 ChIP-seq peaks
- 59% new 419 661 078 Clusters
- 50% new 60 472 672 Metaclusters
How to cite
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. I.S. Yevshin, R.N. Sharipov, T.F. Valeev, A.E. Kel, F.A. Kolpakov. Nucleic Acids Res. 2017 Jan 4;45(D1):D61-D67.
Users may freely use the GTRD database for non-commercial purposes as long as they properly cite it. If you intend to use GTRD for a commercial purpose, please contact email@example.com to arrange a license.
Studies citing GTRD
Eukaryotic and prokaryotic promoter databases as valuable tools in exploring the regulation of gene transcription: a comprehensive overview.
Gene. 2017 Nov 2.
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
Nucleic Acids Res. 2017 Nov 11.
- ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments Nucleic Acids Res. 2017 Nov 8.
- DMS-Seq for In Vivo Genome-wide Mapping of Protein-DNA Interactions and Nucleosome Centers. Cell Reports 2017 Oct 3;21(1):289-300.
- EpiDenovo: a platform for linking regulatory de novo mutations to developmental epigenetics and diseases. Nucleic Acids Research 2017, gkx918
- Genetic variants in ADAMTS13 as well as smoking are major determinants of plasma ADAMTS13 levels. Blood Advances 2017 1:1037-1046;
- Master-regulators driving resistance of non-small cell lung cancer cells to p53 reactivator Nutlin-3. Virtual Biology 2017, 0(4), 1-31.
- Discovering relationships between nuclear receptor signaling pathways, genes, and tissues in Transcriptomine. Sci Signal. 2017 Apr 25;10(476).
- A comprehensive review of web-based non-coding RNA resources for cancer research. Cancer Lett. 2017 Aug 18;407:1-8.
- RUNX1 promote invasiveness in pancreatic ductal adenocarcinoma through regulating miR-93. Oncotarget 2017 Aug 24