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. Kel^1,*, T. Konovalova², T.Waleev³, E.Cheremushkin³, O. Kel-Margoulis¹, E.Wingender^1,4

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.