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

被引：779

作者：

Mathelier, Anthony ^{[1
]}

Zhao, Xiaobei ^{[2
,3
,4
]}

Zhang, Allen W. ^{[1
]}

Parcy, Francois ^{[5
]}

Worsley-Hunt, Rebecca ^{[1
]}

Arenillas, David J. ^{[1
]}

Buchman, Sorana ^{[2
,3
]}

Chen, Chih-yu ^{[1
]}

Chou, Alice ^{[1
]}

Ienasescu, Hans ^{[2
,3
]}

Lim, Jonathan ^{[1
]}

Shyr, Casper ^{[1
]}

Tan, Ge ^{[5
]}

Zhou, Michelle ^{[1
]}

Lenhard, Boris ^{[6
,7
]}

Sandelin, Albin ^{[2
,3
]}

Wasserman, Wyeth W. ^{[1
]}

机构：

[1] Univ British Columbia, Dept Med Genet, Child & Family Res Inst, Ctr Mol Med & Therapeut, Vancouver, BC, Canada

[2] Univ Copenhagen, Bioinformat Ctr, Dept Biol, DK-2200 Copenhagen, Denmark

[3] Univ Copenhagen, Bioinformat Ctr, Biotech Res & Innovat Ctr, DK-2200 Copenhagen, Denmark

[4] Univ N Carolina, Lineberger Comprehens Canc Ctr, Chapel Hill, NC 27599 USA

[5] Univ Grenoble Alpes, CNRS, CEA, Lab Physiol Cellulaire & Vegetale,iRTSV,INRA, F-38054 Grenoble, France

[6] Univ London Imperial Coll Sci Technol & Med, MRC, Ctr Clin Sci, London W12 0NN, England

[7] Univ Bergen, Dept Informat, N-5008 Bergen, Norway

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / D1期

基金：

英国医学研究理事会; 欧洲研究理事会;

关键词：

DNA-BINDING; PROTEIN; IDENTIFICATION; SEQUENCE; BIOINFORMATICS; SPECIFICITIES; RECOGNITION; DOMAINS; BIOLOGY; MURINE;

D O I：

10.1093/nar/gkt997

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：D142 / D147

页数：6

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