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

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Statistics (version 18.06)

Species ChIP-seq experiments Transcription factors ChIP-seq reads Reads aligned ChIP-seq peaks Clusters Metaclusters
Arabidopsis thaliana 345 105 19672668859 12080109334 2837261 2054739 343999
Caenorhabditis elegans 1264 296 23683319859 16982500315 2826585 2005036 379551
Danio rerio 51 20 2139273699 1072924836 1797408 1666839 259705
Drosophila melanogaster 2016 503 69893340390 49980204183 7909465 5617244 1025003
Rattus norvegicus 101 20 5291534576 3158639098 6952157 6603563 865873
Saccharomyces cerevisiae 777 120 12292351248 10061596176 362376 217462 28193
Schizosaccharomyces pombe 171 52 1905140365 1405347268 76700 61379 9138
Mus musculus 5521 432 245723707316 173906764540 512758971 334076411 42985343
Homo sapiens 7239 852 408632740269 321120750790 551164672 345014631 42733385
Total 17485 2400 789234076581 589768836540 1086685595 697317304 88630190

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.

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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.

Studies citing GTRD

User interface

Use cases