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. All data, including the transcription factor – gene interactions, matrix library and command line Match™ program are available for download, for easy integration into your own or third party tools.
Use the newly integrated F-Match algorithm to perform comparative promoter analysis of high-throughput microarray data, identifying the transcription factors most likely to have induced the experimentally observed pattern of gene expression. Or use the integrated DECOD algorithm to identify novel, as-yet-uncharacterized motifs within ChIP-Seq or other data. All algorithms work with the built in promoter library for human, mouse and rat as well as multiple plant species including A. thaliana, O. sativa, and G. max or your own submitted sequences.
Working with human whole genome sequences? TRANSFAC®’s promoter features provide a rich data resource for mapping next generation sequencing variations to transcription factor binding sites characterized in TRANSFAC® including more than 10,000 experimentally verified binding sites, millions of experimental ChIP-Seq and DNase hypersensitivity binding sites refined by prediction, and additional TRANSFAC® regulatory features.