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JASPAR 2014: An Extensively Expanded And Updated Open-access Database Of Transcription Factor Binding Profiles

A. Mathelier, Xiaobei Zhao, A. Zhang, F. Parcy, R. Worsley-Hunt, David J. Arenillas, Sorana Buchman, Chih-Yu Chen, A. Chou, Hans Ienasescu, Jonathan S. Lim, C. Shyr, Ge Tan, M. Zhou, B. Lenhard, A. Sandelin, W. Wasserman
Published 2014 · Computer Science, Biology, Medicine

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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.
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