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

Anthony Mathelier (1) , Xiaobei Zhao (2, 3) , Allen W Zhang (1) , François Parcy (4) , Rebecca Worsley-Hunt (1) , David J Arenillas (1) , Sorana Buchman (2) , Chih-Yu Chen (1) , Alice Chou (1) , Hans Ienasescu (2) , Jonathan Lim (1) , Casper Shyr (1) , Ge Tan (4) , Michelle Zhou (1) , Boris Lenhard (5, 6) , Albin Sandelin (2) , Wyeth W. Wasserman (1)

1 Department of Medical Genetics
2 BRIC - Biotech Research and Innovation Centre
3 UNC Lineberger - Lineberger Comprehensive Cancer Center
4 LPCV - Laboratoire de physiologie cellulaire végétale
5 Computational Regulatory Genomics
6 UiB - Department of Informatics [Bergen]

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.

Mots clés: Transcription factors; database; open access; Vertebrates; plants; insects; nematodes; Fungi; Drosophila melanogaster; Caenorhabditis elegans

Domaines: Biochimie, Biologie Moléculaire

Anthony Mathelier, Xiaobei Zhao, Allen W Zhang, François Parcy, Rebecca Worsley-Hunt, et al.. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.. Nucleic Acids Research, 2014, 42 (1), pp.D142-7. ⟨10.1093/nar/gkt997⟩. ⟨hal-00943558⟩