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

Aziz Khan (1) , Oriol Fornés (2) , Arnaud Stigliani (3) , Marius Gheorghe (1) , Jaime A. Castro-Mondragon (1) , Robin Van der lee (2) , Adrien Bessy (3) , Jeanne Chèneby (4) , Shubhada R. Kulkarni (5) , Ge Tan (6, 7) , Damir Baranasic (6, 7) , David J. Arenillas (2) , Albin Sandelin (8) , Klaas Vandepoele (5) , Boris Lenhard (6, 7, 9) , Benoit Ballester (4) , Wyeth W. Wasserman (2) , François Parcy (3) , Anthony Mathelier (1, 10)

1 NCMM - Centre for Molecular Medicine Norway
2 Department of Medical Genetics
3 LPCV - Physiologie cellulaire et végétale
4 TAGC - Theories and Approaches of Genomic Complexity
5 Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics
6 Computational Regulatory Genomics
7 Institute of Clinical Sciences, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London
8 Bioinformatics Centre
9 Sars International Centre for Marine Molecular Biology
10 Oslo University Hospital Radiumhospitalet

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 tax-onomic 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 .

Keywords: Open Access; Vertebrates; Plants; Nematodes; Transcription factor; Database; Insects; Fungi

Domains: Life Sciences [q-bio]; Life Sciences [q-bio]; Quantitative Methods [q-bio.QM]

Aziz Khan, Oriol Fornés, Arnaud Stigliani, Marius Gheorghe, Jaime A. Castro-Mondragon, et al.. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Research, 2018, 46 (D1), pp.D260-D266. ⟨10.1093/nar/gkx1126⟩. ⟨hal-01646126⟩