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 email@example.com
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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 firstname.lastname@example.org to arrange a license.
Studies citing GTRD
- 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