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.

Comparative promoter analysis of high-throughput microarray data based on TRANSFAC® positional weight matrices is provided in the companion ExPlain™ Analysis System, while the companion Genome Trax™ provides a platform for mapping next generation sequencing variations to transcription factor binding sites characterized in TRANSFAC®.

Benefits

  • 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
  • Build custom transcription regulatory networks out of experimentally demonstrated factor-DNA and factor-factor interactions
  • 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
  • 38,000+ 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
  • 17,000+ miRNA target sites and 900+ miRNA reports
  • 21,000+ transcription factor reports, a subset of which provide GO functional assignments, disease associations and expression pattern assignments
  • 13,843,000+ 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
  • 297,000+ 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 5,000+ positional weight matrices (PWMs) derived from experimentally verified data and 3D homology modeling
  • A tool for matrix comparison
  • A pathway visualization tool for building custom regulatory networks out of experimentally demonstrated factor-DNA and factor-factor interactions

Access Options

Online
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.

Download
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 the TRANSFAC plug-in for CLCbio’s Genomics Workbench software require a 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.

Click here for a table comparison of features available in online vs. download options.

Academic research user? Order now.
Commercial user/clinical, non-profit/academic service provider? Request a quote.

Resources

Support Documents


Research / Whitepapers


Scientific Publications


Training

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


Video Tutorials

Profile Creation
Creating custom profiles for prediction of transcription factor binding sites via Match.
>> Watch video

Composite Model Search
Searching for pairs of transcription factor binding sites.
>> Watch video

MATCH Analysis
Predict binding sites for Transcription Factors in a particular DNA sequence.
>> Watch video

Transcription Factor Search / Result
Easily search for transcription factors, the genes they regulate, linked matrices and much more.
>> Watch video


Archived Webinars

Challenges of Transcription Factor Binding Site Prediction

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