TRANSFAC is a knowledge-base containing published data on eukaryotic transcription factors (and miRNAs), their experimentally-proven binding sites, and regulated genes. The same data also forms the basis of derived positional weight matrices which can be used with the included tools (Match/FMatch/CMsearch) to search DNA sequences for putative transcription factor binding sites. Transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project have been mapped to promoter sequences and complement the binding site data curated from the literature.

Key Capabilities

  • 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
  • Explore detailed reports for transcription factors, their experimentally-characterized binding sites, regulated genes and promoters with mapped regulatory features
  • Download binding fragments and best scoring sites from individual ChIP experiments in FASTA or BED format, or lists of nearest genes, for analysis

Access for database search does not require a personal username and password. But users will need to create a personal account to save data and to use the included tools.

A Yale email address is required to create an account. Register to use TRANSFAC®