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Transcription Regulatory Regions Database (TRRD): A Source of Experimentally Confirmed Data on Transcription Regulatory Regions of Eukaryotic Genes

  • N. KolchanovEmail author
  • E. Ignatieva
  • O. Podkolodnaya
  • E. Ananko
  • I. Stepanenko
  • T. Merkulova
  • T. Khlebodarova
  • V. Merkulov
  • N. Podkolodny
  • D. Grigorovich
  • A. Poplavsky
  • A. Romashchenko
Chapter

Abstract

The goal of creation of the Transcription Regulatory Regions Database (TRRD) was to provide a complete and adequate description of the structure-function organization of transcription regulatory regions in eukaryotic genes. TRRD contains only experimentally confirmed data about (i) transcription factor binding sites; (ii) regulatory units (promoter regions, enhancers, and silencers); and (iii) locus control regions. The main tool for searching TRRD and navigation in it is SRS. TRRD has hierarchically organized vocabularies and thesauruses used for developing specialized data retrieval tools. The current TRRD release contains information about 2308 eukaryotic genes (of them, 34 % are human genes) inputted basing on annotation of 7565 scientific papers. For these genes, the largest in the world sets of experimentally confirmed regulatory units (3439) and transcription factor binding sites (10 045) are collected in TRRD. Of them, 37 % of regulatory units and 38 % of binding sites are related to human genes. This paper characterizes groups of experiments basing on which regulatory units and binding sites are annotated. Examples of TRRD entries are given. The database is available at http://www.bionet.nsc.ru/trrd/.

Key words

database transcription regulation TRRD: Transcription Regulatory Regions Database 

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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • N. Kolchanov
    • 1
    • 2
    Email author
  • E. Ignatieva
    • 1
    • 2
  • O. Podkolodnaya
    • 1
  • E. Ananko
    • 1
  • I. Stepanenko
    • 1
    • 2
  • T. Merkulova
    • 1
    • 2
  • T. Khlebodarova
    • 1
  • V. Merkulov
    • 1
  • N. Podkolodny
    • 1
    • 2
    • 3
  • D. Grigorovich
    • 1
  • A. Poplavsky
    • 1
  • A. Romashchenko
    • 1
  1. 1.Institute of Cytology and GeneticsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia
  3. 3.Institute of Computational Mathematics and Mathematical GeophysicsSiberian Branch of the Russian Academy of SciencesNovosibirskRussia

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