JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles
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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.
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The record
- Venue
- Nucleic Acids Research
- Topic
- Genomics and Chromatin Dynamics
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- —
- Funders
- Seventh Framework ProgrammeH. Lundbeck A/SLundbeckfondenGenome British ColumbiaMichael Smith Health Research BCNational Institute of General Medical SciencesMedical Research CouncilCentre National de la Recherche ScientifiqueNovo NordiskUniversitetet i BergenGenome Canada
- Keywords
- BiologyTranscription factorComputational biologyDNA binding siteGeneticsDatabaseBioinformaticsPromoterComputer scienceGeneGene expression
- Has abstract in OpenAlex
- yes