JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

  • Anthony Mathelier
  • Xiaobei Zhao
  • Allen W. Zhang
  • François Parcy
  • Rebecca Worsley-Hunt
  • David J. Arenillas
  • Sorana Buchman
  • Chih-yu Chen
  • Alice Chou
  • Hans-Ioan Ienasescu
  • Jonathan Lim
  • Casper Shyr
  • Ge Tan
  • Michelle Zhou
  • Boris Lenhard
  • Sandelin, Albin Gustav
  • Wyeth W Wasserman
JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR-the JASPAR CORE subcollection, which contains curated, non-redundant profiles-with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods.
OriginalsprogEngelsk
TidsskriftNucleic Acids Research
Vol/bind42
Sider (fra-til)D142-D147
Antal sider6
ISSN0305-1048
DOI
StatusUdgivet - 2014

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