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

被引：777

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：

欧洲研究理事会; 英国医学研究理事会;

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

共 33 条

[1] Diversity and Complexity in DNA Recognition by Transcription Factors
Badis, Gwenael
Berger, Michael F.
Philippakis, Anthony A.
Talukder, Shaheynoor
Gehrke, Andrew R.
Jaeger, Savina A.
Chan, Esther T.
Metzler, Genita
Vedenko, Anastasia
Chen, Xiaoyu
Kuznetsov, Hanna
Wang, Chi-Fong
Coburn, David
Newburger, Daniel E.
Morris, Quaid
Hughes, Timothy R.
Bulyk, Martha L.
[J]. SCIENCE, 2009, 324 (5935) : 1720 - 1723
[2] Inferring direct DNA binding from ChIP-seq
Bailey, Timothy L.
Machanick, Philip
[J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (17) : e128
[3] MEME SUITE: tools for motif discovery and searching
Bailey, Timothy L.
Boden, Mikael
Buske, Fabian A.
Frith, Martin
Grant, Charles E.
Clementi, Luca
Ren, Jingyuan
Li, Wilfred W.
Noble, William S.
[J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : W202 - W208
[4] Additivity in protein-DNA interactions: how good an approximation is it?
Benos, PV
Bulyk, ML
Stormo, GD
[J]. NUCLEIC ACIDS RESEARCH, 2002, 30 (20) : 4442 - 4451
[5] Berger Michael F., 2006, V338, P245
[6] The Protein Data Bank
Berman, HM
Westbrook, J
Feng, Z
Gilliland, G
Bhat, TN
Weissig, H
Shindyalov, IN
Bourne, PE
[J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 235 - 242
[7] JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
Bryne, Jan Christian
Valen, Eivind
Tang, Man-Hung Eric
Marstrand, Troels
Winther, Ole
da Piedade, Isabelle
Krogh, Anders
Lenhard, Boris
Sandelin, Albin
[J]. NUCLEIC ACIDS RESEARCH, 2008, 36 : D102 - D106
[8] IDENTIFICATION OF NOVEL DNA-BINDING TARGETS AND REGULATORY DOMAINS OF A MURINE TINMAN HOMEODOMAIN FACTOR, NKX-2.5
CHEN, CY
SCHWARTZ, RJ
[J]. JOURNAL OF BIOLOGICAL CHEMISTRY, 1995, 270 (26) : 15628 - 15633
[9] Biopython']python: freely available Python']Python tools for computational molecular biology and bioinformatics
Cock, Peter J. A.
Antao, Tiago
Chang, Jeffrey T.
Chapman, Brad A.
Cox, Cymon J.
Dalke, Andrew
Friedberg, Iddo
Hamelryck, Thomas
Kauff, Frank
Wilczynski, Bartek
de Hoon, Michiel J. L.
[J]. BIOINFORMATICS, 2009, 25 (11) : 1422 - 1423
[10] An integrated encyclopedia of DNA elements in the human genome
Dunham, Ian
Kundaje, Anshul
Aldred, Shelley F.
Collins, Patrick J.
Davis, CarrieA.
Doyle, Francis
Epstein, Charles B.
Frietze, Seth
Harrow, Jennifer
Kaul, Rajinder
Khatun, Jainab
Lajoie, Bryan R.
Landt, Stephen G.
Lee, Bum-Kyu
Pauli, Florencia
Rosenbloom, Kate R.
Sabo, Peter
Safi, Alexias
Sanyal, Amartya
Shoresh, Noam
Simon, Jeremy M.
Song, Lingyun
Trinklein, Nathan D.
Altshuler, Robert C.
Birney, Ewan
Brown, James B.
Cheng, Chao
Djebali, Sarah
Dong, Xianjun
Dunham, Ian
Ernst, Jason
Furey, Terrence S.
Gerstein, Mark
Giardine, Belinda
Greven, Melissa
Hardison, Ross C.
Harris, Robert S.
Herrero, Javier
Hoffman, Michael M.
Iyer, Sowmya
Kellis, Manolis
Khatun, Jainab
Kheradpour, Pouya
Kundaje, Anshul
Lassmann, Timo
Li, Qunhua
Lin, Xinying
Marinov, Georgi K.
Merkel, Angelika
Mortazavi, Ali
[J]. NATURE, 2012, 489 (7414) : 57 - 74

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