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PMID: 24194598 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 42 ·No. Database issue ·2014-01-00 ·Pages D142-7

Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW

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.

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
Chemicals
Transcription Factors
Authors & Affiliations
17 authors, click to expand affiliations / ORCID
Mathelier Anthony
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.
Zhao Xiaobei
Zhang Allen W
Parcy François
Worsley-Hunt Rebecca
Arenillas David J
Buchman Sorana
Chen Chih-yu
Chou Alice
Ienasescu Hans
Lim Jonathan
Shyr Casper
Tan Ge
Zhou Michelle
Lenhard Boris
Sandelin Albin
Wasserman Wyeth W
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkt997
Published
2014-01-00
Epub
2013-00-04
Pages
D142-7
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3965086
Subset
IM
Grants
Medical Research Council · MC_UP_1102/1 · United Kingdom
NIGMS NIH HHS · R01 GM084875 · United States
NIGMS NIH HHS · R01GM084875 · United States
External Links
PubMed source DOI: 10.1093/nar/gkt997 PMC Full Text View journal details
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