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.

An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation

“…Th is may therefore be an evolutionarily conserved feature of the Irx genes. Accordingly, using the Jaspar and CTCF-binding site databases 24,25 , we also found potential CTCF-binding sites in the vicinity of the Xenopus and zebrafi sh Irx genes ( Supplementary Fig. S4 ).…”

The NRF2‐related interactome and regulome contain multifunctional proteins and fine‐tuned autoregulatory loops

“…As NRF2 is important in the inflammation process [9], we also downloaded its interactors and target genes from InnateDB [16]. To predict target genes regulated by NRF2, we applied the transcription factor binding site (TFBS) information of NRF2 from JASPAR [17]. We also included all experimentally verified NRF2 target genes from a large-scale ChIP-Seq profiling study [10].…”

“…We also included all experimentally verified NRF2 target genes from a large-scale ChIP-Seq profiling study [10]. In order to predict transcription factors (TFs) that directly regulate NRF2 transcription, we applied a reverse approach, and queried the regulatory region of the NRF2 gene sequence against all TFBS information found in JASPAR [17]. Additionally, we acquired the list of miRNAs predicted to regulate NRF2 mRNA from miRBase [18].…”

“…We extended this list by including 6 target genes from the manually curated InnateDB and 1054 genes identified in a large-scale ChIP-Seq study [10]. Based on TF-TFBS binding data from JASPAR [17], we further predicted 6426 NRF2 target genes. We found some overlaps between the compiled 7515 target genes: while no genes present in all four sources, we found 1 target gene (COX6C) in three sources (manual curation, ChIP-Seq, JASPAR), and 44 target genes in two sources.…”

“…While there are more than 2300 articles for the keyword 'NRF2' in PubMed (as of January 2012), major protein-protein interaction resources (BioGRID, MINT, STRING, HPRD) contain only a few (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20) interactors for NRF2. Besides one study on the global mapping of binding sites for NRF2 through ChIP-Seq profiling [10] and a specific network modeling approach on Nrf2 regulation in mouse lung [11], there is no large-scale collection of NRF2-regulated target genes.…”