TRANSFAC: Gene Regulation Analysis
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TRANSFAC® is a unique knowledge-base containing published data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes. The extensive compilation of binding sites provides the most comprehensive data set of transcription factor – gene interactions available.  The same data also forms the basis of derived positional weight matrices which can be used with the included Match™ tool to search DNA sequences for putative transcription factor binding sites – a method that is crucial for filling in gaps in the published literature. Integrated transcription factor ChIP-Seq, DNase hypersensitivity and histone methylated intervals from the ENCODE project complement the curated and predicted binding site data. All data, including the transcription factor – gene interactions, matrix library and command line Match™ program are available for download, for easy integration into your own or third party tools.

Use the newly integrated F-Match algorithm to perform comparative promoter analysis of high-throughput microarray data, identifying the transcription factors most likely to have induced the experimentally observed pattern of gene expression. Or use the integrated DECOD algorithm to identify novel, as-yet-uncharacterized motifs within ChIP-Seq or other data. All algorithms work with the built in promoter library for human, mouse and rat as well as multiple plant species including A. thaliana, O. sativa, and G. max or your own submitted sequences.

Working with human whole genome sequences? TRANSFAC®’s promoter features provide a rich data resource for mapping next generation sequencing variations to transcription factor binding sites characterized in TRANSFAC® including more than 10,000 experimentally verified binding sites, millions of experimental ChIP-Seq and DNase hypersensitivity binding sites refined by prediction, and additional TRANSFAC® regulatory features.


  • Quickly access detailed reports for transcription factors and miRNAs, their experimentally-characterized binding sites and regulated genes, and ChIP experiments without tedious and time consuming literature searches
  • Predict transcription factor binding sites within a DNA sequence using your own or TRANSFAC®’s positional weight matrices
  • Model how transcription factors act together to affect gene expression patterns observed in microarray and RNA-Seq experiments in order to understand the cause, not just the effect, of differential expression in response to drug treatment, disease state, environmental conditions, and more
  • Integrate TRANSFAC®’s positional weight matrices into your own or 3rd party tools with the flat file download option

Key Features

  • Interlinked reports connecting transcription factors, their experimentally-characterized binding sites and regulated genes, and associated ChIP fragments
  • 48,000+ transcription factor binding site reports containing details from the primary literature for more than 300 species, with a focus on human, mouse, rat, yeast, and plants
  • 20,000+ miRNA target sites and 1,100+ miRNA reports
  • 22,000+ transcription factor reports, a subset of which provide GO functional assignments, disease associations and expression pattern assignments
  • 14,317,000+ ChIP fragment reports, many with best scoring site prediction for the respective factor, sequences (FASTA) and lists of adjacent genes are downloadable by ChIP Experiment
  • 322,000+ promoter reports including mapped TF-binding sites, ChIP-chip/Seq based TF-binding fragments, histone modification locations, transcription start sites, and single nucleotide polymorphisms (SNPs)
  • The Match™ tool for predicting transcription factor binding sites based on 6,000+ positional weight matrices (PWMs) derived from experimentally verified data and 3D homology modeling
  • Tools for matrix comparison and identification of novel, as-yet-uncharacterized binding motifs
  • A pathway visualization tool for building custom regulatory networks out of experimentally demonstrated factor-DNA and factor-factor interactions

Access Options

An online subscription provides access to the TRANSFAC web interface. Online subscriptions are available at the academic / non-profit lab, department and institution-wide level. The academic / non-profit lab subscription levels require IP plus username/password authentication. IP only authentication is optionally available for the institution-wide subscription level.

A download subscription provides access to flat files containing data for factors, matrices, binding sites, genes, ChIP fragments and other supporting information, as well as command line access to the Match tool. In this way, TRANSFAC data and positional weight matrices may be integrated into your own, or 3rd party, analysis pipelines and tools. However redistribution of, or public access to / display of, the data or results generated by TRANSFAC positional weight matrices is not allowed without prior written consent. Users interested in using TRANSFAC®’s Match tool for prediction of transcription factor binding sites within CLCbio’s Genomics Workbench software must purchase the TRANSFAC TFBS plugin or a TRANSFAC® download subscription. A download subscription does not provide access to the TRANSFAC web interface.

Relational Database Download
A relational database download subscription allows for local installation of the complete TRANSFAC relational database. A local installation allows you to query and extract all fields of TRANSFAC data (including transcription factor disease associations and transcription factor organ/tissue/cell/tumor expression patterns) for integration into your own, or 3rd party, analysis pipelines and tools. However redistribution of, or public access to / display of, the data is not allowed without prior written consent. Relational database download subscriptions do not provide access to the TRANSFAC web interface. MySQL platform is supported.


Support Documents

Research / Whitepapers

Scientific Publications


Feature update 2014.1 – Watch video
Release 2013.3 – Watch video
Release 2012.4 – Watch video

Video Tutorials

MATCH Analysis
Predict binding sites for Transcription Factors in a particular DNA sequence.
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Data Types for Transcription Factor Binding Site Analysis
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Comparative Promoter Analysis of Microarray Data
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Profile Creation
Creating custom profiles for prediction of transcription factor binding sites via Match.
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Composite Model Search
Searching for pairs of transcription factor binding sites.
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Transcription Factor Search / Result
Easily search for transcription factors, the genes they regulate, linked matrices and much more.
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Archived Webinars

Defining Promoter Sequence: Promoter selection and its impact on differential gene expression analysis

Challenges of Transcription Factor Binding Site Prediction

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