title: JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.
abstract: JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release.
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada.
authors.forename: Anthony
authors.initials: A
authors.lastname: Mathelier
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada.
authors.forename: Oriol
authors.initials: O
authors.lastname: Fornes
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada.
authors.forename: David J
authors.initials: DJ
authors.lastname: Arenillas
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada.
authors.forename: Chih-Yu
authors.initials: CY
authors.lastname: Chen
authors.affiliation: Laboratoire Physiologie Cellulaire & Végétale, Université Grenoble Alpes, CNRS, CEA, iRTSV, INRA, 38054 Grenoble, France.
authors.forename: Grégoire
authors.initials: G
authors.lastname: Denay
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada.
authors.forename: Jessica
authors.initials: J
authors.lastname: Lee
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada.
authors.forename: Wenqiang
authors.initials: W
authors.lastname: Shi
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada.
authors.forename: Casper
authors.initials: C
authors.lastname: Shyr
authors.affiliation: Computational Regulatory Genomics, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK.
authors.forename: Ge
authors.initials: G
authors.lastname: Tan
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Worsley-Hunt
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada.
authors.forename: Allen W
authors.initials: AW
authors.lastname: Zhang
authors.affiliation: Laboratoire Physiologie Cellulaire & Végétale, Université Grenoble Alpes, CNRS, CEA, iRTSV, INRA, 38054 Grenoble, France.
authors.forename: François
authors.initials: F
authors.lastname: Parcy
authors.affiliation: Computational Regulatory Genomics, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK b.lenhard@csc.mrc.ac.uk.
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
authors.affiliation: The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, Copenhagen University, Ole Maaloes Vej 5, DK-2200, Denmark albin@binf.ku.dk.
authors.forename: Albin
authors.initials: A
authors.lastname: Sandelin
authors.affiliation: Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, V5Z 4H4, BC, Canada wyeth@cmmt.ubc.ca.
authors.forename: Wyeth W
authors.initials: WW
authors.lastname: Wasserman
mesh_terms: D000818:Animals; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry; D030541:Databases, Genetic; D017434:Protein Structure, Tertiary; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors