Concepedia

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

Anthony Mathelier, Xiaobei Zhao, Allen W. Zhang, François Parcy, Rebecca Worsley-Hunt, David J. Arenillas, Sorana Buchman, Chih‐Yu Chen, Alice Chou, Hans Ienasescu,

Nucleic Acids Research · 2013 · 1K citations · 31 references

DOI Full text

Open access

Concepts

Life SciencesBioinformaticsMolecular BiologyChromatin BiologyGenomicsTranscriptional RegulationChromatinGenomic DatabasesMotif DiscoveryTranscription FactorsChromatin Immunoprecipitation SequencingRegulatory Motif DiscoveryTranscription Factor Binding AnnotationTranscription Factor Binding Site Annotation

TL;DR

JASPAR is the largest open‑access database of matrix‑based nucleotide profiles describing transcription factor binding preferences across multiple species. The updated release derives new and revised profiles primarily from published chromatin immunoprecipitation‑sequencing datasets. The fifth release expands the CORE collection by 30 % with 135 new curated profiles, updates 43 existing ones, enhances the web interface for browsing and searching, and introduces BioPython, R, and Bioconductor packages to facilitate both manual and automated access.

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.