title: JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.
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.
authors.affiliation: Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada, Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Ole Maaloes Vej 5, DK-2200, Denmark, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA, Laboratoire Physiologie Cellulaire & Végétale, Université Grenoble Alpes, CNRS, CEA, iRTSV, INRA, 38054 Grenoble, France, Computational Regulatory Genomics, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK, and Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.
authors.forename: Anthony
authors.initials: A
authors.lastname: Mathelier
authors.forename: Xiaobei
authors.initials: X
authors.lastname: Zhao
authors.forename: Allen W
authors.initials: AW
authors.lastname: Zhang
authors.forename: François
authors.initials: F
authors.lastname: Parcy
authors.forename: Rebecca
authors.initials: R
authors.lastname: Worsley-Hunt
authors.forename: David J
authors.initials: DJ
authors.lastname: Arenillas
authors.forename: Sorana
authors.initials: S
authors.lastname: Buchman
authors.forename: Chih-yu
authors.initials: CY
authors.lastname: Chen
authors.forename: Alice
authors.initials: A
authors.lastname: Chou
authors.forename: Hans
authors.initials: H
authors.lastname: Ienasescu
authors.forename: Jonathan
authors.initials: J
authors.lastname: Lim
authors.forename: Casper
authors.initials: C
authors.lastname: Shyr
authors.forename: Ge
authors.initials: G
authors.lastname: Tan
authors.forename: Michelle
authors.initials: M
authors.lastname: Zhou
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
authors.forename: Albin
authors.initials: A
authors.lastname: Sandelin
authors.forename: Wyeth W
authors.initials: WW
authors.lastname: Wasserman
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D006801:Humans; D020407:Internet; D051379:Mice; D056510:Position-Specific Scoring Matrices; D050436:Regulatory Elements, Transcriptional; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors