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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp950
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

Elodie Portales-Casamar1, Supat Thongjuea2, Andrew T. Kwon1, David Arenillas1, Xiaobei Zhao3, Eivind Valen3, Dimas Yusuf1, Boris Lenhard2,*, Wyeth W. Wasserman1,* and Albin Sandelin3,*

1Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver BC, V5Z 4H4, Canada, 2Computational Biology Unit – Bergen Center for Computational Science, and Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway and 3The Bioinformatics Centre, Department of Biology and Biomedical Research and Innovation Centre, Copenhagen University, Ole Maaloes Vej 5, DK-2200, Denmark

*To whom correspondence should be addressed. Tel: +47 555 84362; Fax: +47 555 84295; Email: boris.lenhard{at}bccs.uib.no

Correspondence may also be addressed to Wyeth W. Wasserman. Tel: +1 604 875 3812; Fax: +1 604 875 3819; Email: wyeth{at}cmmt.ubc.ca

Correspondence may also be addressed to Albin Sandelin. Tel: +45 353 21 285; Fax: +45 353 21281; Email: albin{at}binf.ku.dk

Received September 15, 2009. Revised October 11, 2009. Accepted October 12, 2009.

JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database to date: the database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. The introduction of a yeast division brings the convenience of JASPAR to an active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family. The changes in the database set the system ready for more rapid acquisition of new high-throughput data sources. Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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