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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Workflow
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.

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Statistics
version 16.07

  • 5078 ChIP-seq experiments
  • 542 Transcription factors
  • 183 770 420 298 ChIP-seq reads
  • 146 855 318 517 Reads aligned
  • 296 112 088 ChIP-seq peaks
  • 176 007 357 Clusters
  • 30 178 267 Metaclusters
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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 Research, published online: October 24, 2016)

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.

User interface

Use cases