JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles-Reference-Cited by-同舟云学术

JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles

Published:2021-11-30 Issue:D1 Volume:50 Page:D165-D173
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Castro-Mondragon Jaime A¹^ORCID,Riudavets-Puig Rafael¹^ORCID,Rauluseviciute Ieva¹^ORCID,Berhanu Lemma Roza¹^ORCID,Turchi Laura²^ORCID,Blanc-Mathieu Romain²^ORCID,Lucas Jeremy²^ORCID,Boddie Paul¹,Khan Aziz³^ORCID,Manosalva Pérez Nicolás⁴⁵^ORCID,Fornes Oriol⁶^ORCID,Leung Tiffany Y⁶^ORCID,Aguirre Alejandro⁶^ORCID,Hammal Fayrouz⁷^ORCID,Schmelter Daniel⁸,Baranasic Damir⁹¹⁰,Ballester Benoit⁷^ORCID,Sandelin Albin¹¹^ORCID,Lenhard Boris⁹¹⁰^ORCID,Vandepoele Klaas⁴⁵¹²^ORCID,Wasserman Wyeth W⁶^ORCID,Parcy François²^ORCID,Mathelier Anthony¹¹³^ORCID

Affiliation:

1. Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway

2. Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrsF-38054, Grenoble, France

3. Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA94305, USA

4. Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium

5. VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium

6. Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, 950 W 28th Ave, Vancouver, BC V5Z 4H4, Canada

7. Aix Marseille Univ, INSERM, TAGC, Marseille, France

8. UCSC Genome Browser, University of California Santa Cruz, Santa Cruz, CA95060, USA

9. MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK

10. Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK

11. The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK2200 Copenhagen N, Denmark

12. Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Ghent, Belgium

13. Department of Medical Genetics, Institute of Clinical Medicine, University of Oslo and Oslo University Hospital, Oslo, Norway

Abstract

Abstract JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data.

Funder

Norwegian Research Council

Helse Sør-Øst

University of Oslo

Norwegian Cancer Society

GRAL program

CBH-EUR-GS

CNRS Prime80

NHGRI

Ghent University

Provence-Alpes-Côte d’Azur Regional Council

Institut National de la Santé et de la Recherche Médicale