Interlinked reports connecting transcription factors, their experimentally-characterized binding sites and regulated genes, as well as promoter reports with mapped annotated TF-binding sites and high-throughput data (ChIP-seq etc.)
Enhancer reports displaying genes with which promoters the enhancer interacts, tissues and cell types/lines the enhancer is active in, and genomic regions such as histone modification sequences, DNase I hypersensitivity sites, and transcription factor binding sites that overlap with the enhancer.
More than 70,000 site reports containing details from the primary literature for more than 300 species, with a focus on human, mouse, rat, yeast, and plants.
More than 48,000 transcription factor (and 1,700 miRNA) reports, a subset of which provide GO functional assignments, disease associations and expression pattern assignments.
More than 68,000 manually annotated transcription factor–site interactions; plus more than 74,000 miRNA-target site interactions.
More than 2,000 high-throughput TFBS ChIP experiment reports comprising 91M transcription factor bound fragments/intervals, many of which have been annotated with the best-scoring binding site and neighbouring genes, as well as 161 DNase hypersensitivity ChIP-Seq experiments comprising 15M fragments and 1M histone modification fragments.
More than 10,000 positional weight matrices, to be used by MatchTM, FMatch, CMsearch and a number of geneXplain bricks to predict TF binding sites.
More than 360,000 promoter reports for human and nine other organisms, including transcription start sites, CpG islands, single nucleotide polymorphisms (SNPs) and various other annotations.
Including tools for TF-binding site prediction, de novo motif identification, matrix comparison and miRNA regulator identification.
Further, including a pathway visualization tool for building custom regulatory networks out of experimentally demonstrated factor-DNA and factor-factor interactions, as well as a functional analysis tool for identification of shared attributes in an analyzed gene set.