TRANSFAC® is a unique knowledge-base containing published data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes. The extensive compilation of binding sites provides the most comprehensive data set of transcription factor – gene interactions available. The same data also forms the basis of derived positional weight matrices which can be used with the included Match™ tool to search DNA sequences for putative transcription factor binding sites – a method that is crucial for filling in gaps in the published literature. Integrated transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project complement the curated and predicted binding site data.
Comparative promoter analysis of high-throughput microarray data based on TRANSFAC® positional weight matrices is provided in the companion ExPlain™ Analysis System, while the companion Genome Trax™ provides a platform for mapping next generation sequencing variations to transcription factor binding sites characterized in TRANSFAC®.