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

Abstract

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.

Figure 1.

Examples of SELEX-derived matrix profiles replaced by ChIP-seq-derived profiles. (A) The previous MYCN matrix profile (MA0104.1) derived by DNA SELEX. (B) The new MYCN profile (MA0104.2) derived from ChIP-seq binding shows general agreement with the SELEX profile, with additional information derived from hundreds of sites at flanking positions. (C) The previous KLF4 profile (MA0039.1) is an example of SELEX-derived profile that did not correspond well to the handful of individually characterized KLF4 sites. (D) The new KLF profile derived from ChIP-seq data (13) shows a dramatic increase in information content and a good agreement with individually characterized binding sites.