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

TLDR

JASPAR is the leading open‑access database of DNA‑binding matrix profiles for transcription factors and other sequence‑specific DNA‑interacting proteins. The authors added a yeast division and updated the database to enable rapid incorporation of new high‑throughput data, expanding its usability for active research communities. The release incorporates ChIP‑seq and ChIP‑chip derived profiles, 177 yeast TF binding profiles, versioned matrices with 12 % updated models, and three new special collections from alternative high‑throughput methods. The fourth release now contains 457 curated, non‑redundant profiles, improves TF family classification with a new DNA‑binding domain nomenclature, and adds a mammalian TF catalog extending coverage to related structural families.

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.