Welcome on the TRANSFAC page of geneXplain,
the world-wide exclusive distributor of this unique information resource!

Release 2016.2 provides the largest matrix library available:
More than 6500 positional weight matrices!
More than 30 million sites from high-throughput approaches!
What is TRANSFAC® about?
TRANSFAC® is the database of eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles. Dating back to a very early compilation, it has been carefully maintained and curated since then and became the gold standard in the field, which can be made use of when applying the geneXplain platform. In particular its library of positional weight matrices is a unique collection of DNA-binding models, suitable for a comprehensive analysis of genomic sequences for potential transcription factor binding sites (TFBSs).
You can use TRANSFAC® as encyclopedia of transcriptional regulation, or as a tool to identify potential TFBSs. The latter can be done with the proven tool MatchTM, or with any of the respective modules in the geneXplain platform.

Learn more about promoter analysis with TRANSFAC® in the geneXplain platform.

The structure
The core of TRANSFAC comprises contents of two domains: One documents TF binding sites, usually in promoters or enhancers. The other describes the binding proteins (TFs).
On top of each of these two domains, an abstract view on its contents is provided:
Binding sites referring to the same TF are merged into a positional weight matrix. Such a matrix reflects the frequency with which each nucleotide is found in each position of this TF's binding sites and, thus, the base preference in each position.
Transcription factors are subsumed to classes, based on the general properties of their DNA-binding domains. This early attempt has been expanded to a comprehensive TF classification, the latest version of which can be found here.
TRANSFAC concept
Organization of TRANSFAC® contents.
(Click for an enlarged view.)

Further information:
TRANSFAC® Flyer (download; pdf, 0.63 MB)
TRANSFAC® Statistics 2016.2
TRANSFAC® Documentation (2012.1) (download; pdf, 0.71 MB)
TRANSFAC® Video (at YouTube)
See also the TRANSFAC® entry at Wikipedia.
More about TRANSFAC as a scientific project and its history on the pages of Edgar Wingender.
TRANSFAC® is a registered trademark of QIAGEN.

Recent TRANSFAC® applications (selected):
Get a picture of TRANSFAC®
TRANSFAC screenshot
Click to enlarge the plain flat file entry of a Site entry. © Copyright 2016 QIAGEN GmbH. All rights reserved.

Among its key features are:
Interlinked reports connecting transcription factors, their experimentally-characterized binding sites and regulated genes, and associated ChIP fragments
More than 68,000 regulatory site reports containing details from the primary literature for more than 300 species, with a focus on human, mouse, rat, yeast, and plants
About 24,500 transcription factor (and miRNA) reports, a subset of which provide GO functional assignments, disease associations and expression pattern assignments
More than 64,000 transcription factor – site interactions, manually annotated and quality-checked; plus more than 57,000 microRNA-target site interactions
More than 30,300,000 ChIP fragment reports comprising transcription factor bound fragments (13.8 million), DNAse I hypersensitive regions (15.4M), histone modification fragments (1M) and DNA methylation fragments (52K)
More than 6500 positional weight matrices, to be used by MatchTM and a number of geneXplain bricks to predict TF binding sites.
More than 323,000 promoter reports including transcription start sites, CpG islands and single nucleotide polymorphisms (SNPs)
A pathway visualization tool for building custom regulatory networks out of experimentally demonstrated factor-DNA and factor-factor interactions
More detailed statistics can be obtained here.

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.
Use TRANSFAC®'s positional weight matrices as an integral part of the geneXplain platform.
Mail us to get a quote: info(at)!



TRANSFAC key publications:

Kaplun, A., Krull, M., Lakshman, K., Matys, V., Lewicki, B., Hogan, J.D. (2016) Establishing and validating regulatory regions for variant annotation and expression analysis. BMC Genomics 17 (Suppl. 2):393. PubMed.

Wingender, E. (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief. Bioinform. 9:326-332. PubMed.

Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K., Voss, N., Stegmaier, P., Lewicki-Potapov, B., Saxel, H., Kel, A.E., Wingender, E. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34:D108-D110. PubMed.

Kel, A.E., Gössling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V., Wingender, E. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31:3576-3579. PubMed

Wingender, E., Dietze, P., Karas, H., Knüppel, R. (1996) TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res. 24:238-241. PubMed

Knüppel, R., Dietze, P., Lehnberg, W., Frech, K., Wingender, E. (1994) TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins. J. Comput. Biol. 1:191-198. PubMed

Wingender, E. (1988) Compilation of transcription regulating proteins. Nucleic Acids Res. 16:1879-1902. PubMed