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Oxford University Press, Nucleic Acids Research, D1(42), p. D142-D147, 2013

DOI: 10.1093/nar/gkt997

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

Journal article published in 2013 by Anthony Mathelier, Xiaobei Zhao, Allen W. Zhang, François Parcy ORCID, Rebecca Worsley-Hunt, David J. Arenillas, Sorana Buchman, Chih-Yu Chen, Alice Chou, Hans Ienasescu, Jonathan Lim, Casper Shyr, Ge Tan, Michelle Zhou, Boris Lenhard ORCID and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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.