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

• DOI: 10.17615/gepd-y994
• Publication Date: 2013-11-04
• Authors: Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W; Parcy, François; Worsley-Hunt, Reb...; Arenillas, David J; Buchman, Sorana; Chen, Chih-Yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W.
• Keywords: 0301 basic medicine; base de séquences; I. Nucleic acid sequence, structure and regulation; Bioinformatics; libre accès; [SDV.BBM]Life Sciences [q-bio]/Biochemistry; Arabidopsis; :Matematikk og naturvitenskap: 400::Basale biofag: 470::Bioinformatikk: 475 [VDP]; éléments de régulation transcriptionnelle; Databases; site de liaison; Mice; 03 medical and health sciences; Genetic; Databases, Genetic; Transcription factors; Animals; Humans; Position-Specific Scoring Matrices; [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology; Regulatory Elements, Transcriptional; insects; Caenorhabditis elegans; Molecular Biology; database; open access; 020; Internet; 0303 health sciences; Binding Sites; plants; Fungi; VDP::Mathematics and natural scienses: 400::Basic biosciences: 470::Bioinformatics: 475; Regulatory Elements; VDP::Matematikk og naturvitenskap: 400::Basale biofag: 470::Bioinformatikk: 475; arabidopsis; Drosophila melanogaster; logiciel libre; Vertebrates; nematodes; Bio-informatique; Transcriptional; :Mathematics and natural scienses: 400::Basic biosciences: 470::Bioinformatics: 475 [VDP]; facteur de transcription; Transcription Factors

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.