MolBio Licensed Tools: TRANSFAC/Match
TRANSFAC is the database of eukaryotic transcription factors, their experimentally determined genomic binding sites, derived DNA-binding motifs (PWMs), and target genes. It can be used as encyclopedia of transcriptional regulation, or as a tool to identify potential transcription factor binding sites (Match/FMatch/CMsearch). Integrated transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project complement the curated binding site data. Moreover, TRANSFAC contains experimental data on miRNAs and their target sites.
- 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.