v17.04

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 17.04

  • 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
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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 Res. 2017 Jan 4;45(D1):D61-D67.

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