Predicting transcriptional regulators for gene sets

 

If you have a gene group (e.g. from gene expression studies) and you are interested whether there are any transcription factor binding sites enriched in the promoters of your gene group, this site may help you.

 

The prediction of which transcription factors regulate a group of target genes is based on affinities of the transcription factors to the putative promotors of the genes. The affinities have been precalculated based on the available positional frequency matrices for the transcription factors [1].

 

If you use our method, please cite [2], where we provide details on TransFind implementation and its evaluation.

 

Select "Start prediction" in the main menu to submit your gene group (and, if you wish, a background gene group). Select "About TransFind" if you want to learn more about the algorithms used.

 


Figure: Flow of Information

 

Authors:

TransFind has been developed in a cooperation between Szymon M. Kiełbasa, Holger Klein, Helge Roider, Martin Vingron (Max-Planck-Institute of Molecular Genetics, Berlin, Germany), and Nils Blüthgen (Institute of Pathology at Charite, Berlin and Institute of Theoretical Biology, Humboldt University, Berlin, Germany).

 

Literature:

1) Roider HG, Kanhere A, Manke T, Vingron M. Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics. 2007 Jan 15;23(2):134-41. Epub 2006 Nov 10.

2) Kiełbasa SM, Klein H, Roider HG, Vingron M, Blüthgen N. TransFind--predicting transcriptional regulators for gene sets. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W275-80.


Acknowledgement:

Funding of the work on this website has been provided from BMBF (through FORSYS partner initiative), from EU (CancerSys project), the German National Genome Research Network (NGFN-Plus #01GS0815), and the IRTG for Genomics and Systems Biology of Molecular Networks.


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