About Transfind

Given a set of genes, Transfind predicts transcription factors with affinities to the gene promoters significantly higher compared to a background set of genes. It provides an easy-to-use, reliable and fast interface for performing the calculation.

Transfind has been developed in a cooperation between Szymon M. Kiełbasa, Holger Klein, Helge Roider (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).

 

 

Data/software sources:

The putative promoter sequences were extracted from Ensembl version 57 [1].  For each gene we chose the longest transcript and defined the transcription start site as the first base of this transcript. The sequences starting at 800nt upstream to 200nt downstream of TSS, or 300nt upstream to 100nt downstream were extracted unsing custom software.

Binding affinities were predicted for all vertebrate positional frequency matrices available in Transfac (version 2009.4) [2] using a custom implementation of the TRAP algorithm developed in the group of Martin Vingron [3].

Overrepresentation of high-affinity promoters for the transcription factors among the group of interesting genes is tested with a multiple-testing-corrected (FDR) version of the Fisher's excact test which has been developed by us [4].

The logo of Transfind as well as all displayed sequence logos were calculated using code from weblogo based on the idea of [5].

The website uses Joomla! as content management system, which also handles user IDs. No login is required to use the algorithm.

 

References:

1) Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM. Ensembl's 10th year. Nucleic Acids Res. 2009 Nov 11. [Epub ahead of print]

2) Matys V, Kel-Margoulis OV, 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 AE, Wingender E.. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D108-10.

3) Manke T, Roider HG, Vingron M. Statistical modeling of transcription factor binding affinities predicts regulatory interactions. PLoS Comput Biol. 2008 Mar 21;4(3):e1000039.

4) Blüthgen N, Kiełbasa SM, Herzel H. Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res. 2005 Jan 12;33(1):272-9.

5) Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990 Oct 25;18(20):6097-100.

 

Contact:

There is absolutely no warranty for TransFind. If you think that something is not working, please contact us at: nils.bluethgen [oops, remove this part] charite.de, holger.klein [oops, remove this part] molgen.mpg.de, or at szymon.kielbasa [oops, remove this part] molgen.mpg.de.