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

Aziz Khan; Oriol Fornés; Arnaud Stigliani; Marius Gheorghe; Jaime A. Castro-Mondragon; Robin Van der lee; Adrien Bessy; Jeanne Chèneby; Shubhada R. Kulkarni; Ge Tan; Damir Baranasic; David J. Arenillas; Albin Sandelin; Klaas Vandepoele; Boris Lenhard; Benoit Ballester; Wyeth Wasserman; François Parcy; Anthony Mathelier

doi:10.1093/nar/gkx1126

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 Wasserman ² François Parcy ³ Anthony Mathelier ^{1, 10, *}

* Auteur correspondant

1 Centre for Molecular Medicine Norway

2 Department of Medical Genetics

3 LPCV - Laboratoire de physiologie cellulaire végétale

4 TAGC - Technologies avancées pour le génôme et la clinique

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

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 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 : Insects Plants Vertebrates Open Access Database Transcription factor Nematodes Fungi

Type de document :

Article dans une revue

Nucleic Acids Research, Oxford University Press, 2018, 46, pp.D260-D266. 〈10.1093/nar/gkx1126〉

Domaine :

Sciences du Vivant [q-bio]

Sciences du Vivant [q-bio] / Bio-Informatique, Biologie Systémique [q-bio.QM]

Liste complète des métadonnées

https://hal-amu.archives-ouvertes.fr/hal-01646126
Contributeur : Benoit Ballester <>
Soumis le : jeudi 23 novembre 2017 - 11:54:02
Dernière modification le : jeudi 28 juin 2018 - 09:51:49

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