TRANSFAC DOWNLOAD

Download TRANSFAC and do whatever you like

Introduction

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.