JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Abstract JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASP...

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Bibliographic Details
Published in:Nucleic acids research 2018-01, Vol.46 (D1), p.D260-D266
Main Authors: Khan, Aziz, Fornes, Oriol, Stigliani, Arnaud, Gheorghe, Marius, Castro-Mondragon, Jaime A, van der Lee, Robin, Bessy, Adrien, Chèneby, Jeanne, Kulkarni, Shubhada R, Tan, Ge, Baranasic, Damir, Arenillas, David J, Sandelin, Albin, Vandepoele, Klaas, Lenhard, Boris, Ballester, Benoît, Wasserman, Wyeth W, Parcy, François, Mathelier, Anthony
Format: Article
Language:English
Subjects:
Animals
Binding Sites - genetics
Database Issue
Databases, Genetic
Genomics
Humans
Internet
Life Sciences
Plants - genetics
Plants - metabolism
Position-Specific Scoring Matrices
Protein Binding - genetics
Quantitative Methods
Transcription Factors - metabolism
User-Computer Interface
Vertebrates - genetics
Vertebrates - metabolism
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Summary:Abstract JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkx1126