v18.06

GTRD
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 ivan@nulldote.ru

Start » Documentation » Download » Previous release »

Workflow
How was it 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 »

How to cite

License

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 ivan@nulldote.ru to arrange a license.

Statistics (version 18.06)

Species ChIP-seq experiments Transcription factors ChIP-seq reads Reads aligned ChIP-seq peaks Clusters Metaclusters
Arabidopsis thaliana 345 105 19,7 · 109 12,1 · 109 2,8 · 106 2,1 · 106 343,9 · 103
Caenorhabditis elegans 1264 296 23,7 · 109 16,9 · 109 2,8 · 106 2,0 · 106 379,6 · 103
Danio rerio 51 20 2,1 · 109 1,1 · 109 1,8 · 106 1,7 · 106 259,7 · 103
Drosophila melanogaster 2016 503 69,9 · 109 49,9 · 109 7,9 · 106 5,6 · 106 1,0 · 106
Rattus norvegicus 101 20 5,3 · 109 3,2 · 109 6,9 · 106 6,6 · 106 865,9 · 103
Saccharomyces cerevisiae 777 120 12,3 · 109 10,1 · 109 362,4 · 103 217,5 · 103 28,2 · 103
Schizosaccharomyces pombe 171 52 1,9 · 109 1,4 · 109 76,7 · 103 61,4 · 103 9,1 · 103
Mus musculus 5521 432 245,7 · 109 173,9 · 109 512,8 · 106 334,1 · 106 42,9 · 106
Homo sapiens 7239 852 408,6 · 109 321,1 · 109 551,2 · 106 345,0 · 106 42,7 · 106
Total 17485 2400 789,2 · 109 589,8 · 109 1,1 · 109 697,3 · 106 88,6 · 106

Studies citing GTRD

User interface

Use cases