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The Molecular Biology Database Collection: an updated compilation of biological database resources

Authors
Journal
Nucleic Acids Research
0305-1048
Publisher
Oxford University Press
Publication Date
Keywords
  • Article
Disciplines
  • Computer Science

Abstract

OP-NARE130997 142..147 JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles Anthony Mathelier1, Xiaobei Zhao2,3, Allen W. Zhang1, Franc¸ois Parcy4, Rebecca Worsley-Hunt1, David J. Arenillas1, Sorana Buchman2, Chih-yu Chen1, Alice Chou1, Hans Ienasescu2, Jonathan Lim1, Casper Shyr1, Ge Tan4, Michelle Zhou1, Boris Lenhard5,6,*, Albin Sandelin2,* and Wyeth W. Wasserman1,* 1Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada, 2Department of Biology and Biotech Research and Innovation Centre, The Bioinformatics Centre, Copenhagen University, Ole Maaloes Vej 5, DK-2200, Denmark, 3Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA, 4Laboratoire Physiologie Cellulaire & Ve´ge´tale, Universite´ Grenoble Alpes, CNRS, CEA, iRTSV, INRA, 38054 Grenoble, France, 5Computational Regulatory Genomics, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK, and 6Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway Received September 15, 2013; Accepted October 3, 2013 ABSTRACT JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of tran- scription 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,

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