Composite Module Analyst (CMA)

Defining promoter models based on the composition of transcription factor binding sites and their pairs.

 

Composite modules (CM) - combinations of binding sites common for promoters of functionally related genes and responsible for the major component of the gene expression pattern of these genes.

 

 


 

 

Algorithm


 

 

Example


 

 

Run CMA

 

Authors: A. Kel1,*, T. Konovalova2, T.Waleev3, E.Cheremushkin3, O. Kel-Margoulis1, E.Wingender1,4

1 BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany;
2
Institute of Cytology and Genetics, Novosibirsk, Russia ;
3 A.P. Ershov's Institute of Informatics Systems, 6, Lavrentiev ave., 630090 Novosibirsk, Russia;
4 Dept. Bioinformatics, UKG/Univ. Göttingen, Goldschmidstr. 1, 37077 Göttignen, Germany

 

acknowledgements

Authors would like to thank all co-workers of the BIOBASE GmbH who have been contributing to the integration of CMA into the ExPlain™ system. Parts of the work were funded by grant of the German Ministry of Education and Research (BMBF) together with BioRegioN GmbH “BioProfil”, grant no. 0313092; “Intergenomics” Project, Grant No. 031U110C/031U210C; by European Commission under FP6-"Life sciences, genomics and biotechnology for health" contract LSHG-CT-2004-503568 “COMBIO”, by European Commission under “Marie Curie research training networks” contract MRTN-CT-2004-512285 “TRANSISTOR”, and by INTAS grant No:03-51-5218.

Development was sponsored by BIOBASE GmbH  and coding was done with the help of BioRainbow Co.