JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles - PubMed (original) (raw)

. 2014 Jan;42(Database issue):D142-7.

doi: 10.1093/nar/gkt997. Epub 2013 Nov 4.

Xiaobei Zhao, Allen W Zhang, François Parcy, 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, Albin Sandelin, Wyeth W Wasserman

Affiliations

• PMID: 24194598
• PMCID: PMC3965086
• DOI: 10.1093/nar/gkt997

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

Anthony Mathelier et al. Nucleic Acids Res. 2014 Jan.

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.

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Figures

Figure 1.

Screenshot of an example TFBS profile in new layout.

Figure 2.

TFBSs with two different profiles. (A) JUN, (B) JUND, (C) Nkx2-5 and (D) RAV1.

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