TRANSFAC®
Covering transcription factors and DNA binding sites for gene regulation studies.
TRANSFAC® is an internationally unique knowledgebase containing data on eukaryotic transcription factors, their experimentally-proven binding sites, and regulated genes. Based on its broad compilation of binding sites, positional weight matrices are derived which can be used with the included Match™ tool to search DNA sequences for predicted transcription factor binding sites. Promoter analysis of high-throughput data based on TRANSFAC® positional weight matrices is provided in the companion ExPlain™ Analysis System.
Benefits
• Quickly access detailed reports for transcription factors, 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
• 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
• 33,000+ 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+ transcription factor reports (including miRNAs), a subset of which provide GO functional assignments, disease associations and expression pattern assignments
• 1,800,000+ ChIP fragment reports that include the best scoring site prediction for the respective factor as well as downloadable sequences and gene lists
• 277,000+ promoter reports including ChIP-chip/Seq based histone modification locations, transcription start sites, and single nucleotide polymorphisms (SNPs)
• The Match™ tool for predicting transcription factor binding sites based on 1,500+ positional weight matrices (PWMs) derived from experimentally verified data
• 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 Download
A relational download subscription allows for local installation of the complete TRANSFAC relational database and web interface. A local installation allows you to query and extract all fields of TRANSFAC data (including transcription factor disease associations and best-supported TF binding sites within ChIP-Seq fragments) 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 download subscriptions are only available at the institution-wide level. MySQL and Oracle platforms are supported.
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