TRANSFAC® is a unique knowledge-base containing published data on eukaryotic transcription factors, their experimentally-proven binding sites, and regulated genes. Based on its broad compilation of binding sites, positional weight matrices are derived which can be used with the included Match™ tool to search DNA sequences for predicted transcription factor binding sites. Promoter analysis of high-throughput 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®.
Transcription factors are recognized as important components of signaling cascades controlling all types of normal cellular processes as well as response to external stimulus, conditions of disease drug treatment, and more. While functional studies of transcription factors can provide indirect clues to the genes regulated by a single transcription factor under a specific set of experimental conditions, it’s only through transcription factor binding site analysis that we can (1) understand the mechanism of regulation, including coordinate regulation by multiple transcription factors acting together, and (2) effectively identify and characterize mutations that disrupt the regulatory mechanism. As there are comparatively few experimentally characterized binding sites relative to the total number of expected binding sites, the ability to reliably predict as yet uncharacterized binding sites is a critical and unparalleled tool in the quest to understand normal as well as disease processes.