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

Nucleic Acids Res. 2014 Jan;42(Database issue):D142-7. doi: 10.1093/nar/gkt997. Epub 2013 Nov 4.

Abstract

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Arabidopsis / genetics
  • Binding Sites
  • Caenorhabditis elegans / genetics
  • Databases, Genetic*
  • Drosophila melanogaster / genetics
  • Humans
  • Internet
  • Mice
  • Position-Specific Scoring Matrices
  • Regulatory Elements, Transcriptional*
  • Transcription Factors / metabolism*

Substances

  • Transcription Factors