TRANSFAC is the database of eukaryotic transcription factors, their genomic binding sites, and DNA-binding profiles. Its library of positional weight matrices is a unique collection of DNA-binding models, suitable for a comprehensive analysis of genomic sequences for potential transcription factor binding sites. The core of TRANSFAC comprises contents of two domains: One documents TF binding sites, usually in promoters or enhancers. The other describes the binding proteins.
- Predict TF binding sites or composite elements within single DNA sequences with Match and CMsearch, using matrices (PWMs) from TRANSFAC or your own
- Analyze microarray, ChIP-seq and RNA-seq data for over-represented TF-binding sites (FMatch/Step-by-step analysis)
- Find de novo motifs in sequence sets with the DECOD algorithm and compare them against TRANSFAC matrices
- Analyze gene sets for the presence of shared miRNA target sites
- Build custom transcription regulatory networks from experimentally demonstrated factor-DNA and factor-factor interactions
- Access detailed reports for transcription factors, their experimentally-characterized binding sites, regulated genes and promoters (with mapped regulatory features)
- Download binding fragments from individual ChIP experiments in fasta or bed format, or lists of nearest genes, for analysis with FMatch or other tools.