GTRD: A database of transcription factor binding sites identified by ChIP-seq experiments

Ivan Yevshin, Ruslan Sharipov, Tagir Valeev, Alexander Kel, Fedor Kolpakov

Research output: Contribution to journalArticlepeer-review

108 Citations (Scopus)

Abstract

GTRD - Gene Transcription Regulation Database (http://gtrd.biouml.org) - is a database of transcription factor binding sites (TFBSs) identified by ChIPseq experiments for human and mouse. Raw ChIPseq data were obtained from ENCODE and SRA and uniformly processed: (i) reads were aligned using Bowtie2; (ii) ChIP-seq peaks were called using peak callers MACS, SISSRs, GEM and PICS; (iii) peaks for the same factor and peak callers, but different experiment conditions (cell line, treatment, etc.), were merged into clusters; (iv) such clusters for different peak callers were merged into metaclusters that were considered as non-redundant sets of TFBSs. In addition to information on location in genome, the sets contain structured information about cell lines and experimental conditions extracted from descriptions of corresponding ChIP-seq experiments. A web interface to access GTRD was developed using the BioUML platform. It provides: (i) browsing and displaying information; (ii) advanced search possibilities, e.g. search of TFBSs near the specified gene or search of all genes potentially regulated by a specified transcription factor; (iii) integrated genome browser that provides visualization of the GTRD data: read alignments, peaks, clusters, metaclusters and information about gene structures from the Ensembl database and binding sites predicted using position weight matrices from the HOCOMOCO database.

Original languageEnglish
Pages (from-to)D61-D67
Number of pages7
JournalNucleic Acids Research
Volume45
Issue numberD1
DOIs
Publication statusPublished - 4 Jan 2017

Keywords

  • Animals
  • Binding Sites
  • Cell Line
  • Databases, Genetic
  • Humans
  • Immunoprecipitation
  • Mice
  • Regulatory Elements, Transcriptional
  • Sequence Analysis, DNA
  • Transcription Factors/metabolism
  • PROTEIN-DNA INTERACTIONS
  • RESOLUTION
  • GENOME
  • ARCHIVE
  • RECEPTOR GENE

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