TRANSFAC® Download academic lab license

TRANSFAC® flat file download (including the databases TRANSCompel® and TRANSProTM) contains eukaryotic transcription factors (and miRNAs), their experimentally determined genomic binding sites and consensus DNA-binding motifs (PWMs), as well as data on combinatorial gene regulation and factor-factor interaction. Promoters, enhancers and silencers annotated with transcription factor ChIP-Seq, DNase hyper-sensitivity and histone methylated intervals from the ENCODE project and from other sources complement the manually curated binding site data.

Key features:

• Intended for Bioinformaticians

• No installation is needed – just download and unzip archives

• Data files are provided in DAT and JSON formats

• Promoters are provided in the DAT and GTF formats

• Direct data access without user interface: data extraction is possible via Perl scripts or other programs written by the user

• Java-based tools for TFBS search (Match Library) are accessible via a command line

• For use with customer tools and incorporation into user-specific pipelines

What you will get:

• Based on the positional weight matrices (PWMs) transcription factor binding sites can be predicted in regulatory regions.

• In the TRANSFAC® flat file download, the tools of the MatchTM Library can be used on command line or the PWMs can be used with tools of the user.