Gesellschaft für Informatik e.V.

Lecture Notes in Informatics

German Conference on Bioinformatics 2005 (GCB 2005), 5.-7. October 2005, Hamburg, Germany P-71, 63-75 (2005).



Andrew Torda, Stefan Kurtz, Matthias Rarey (eds.)


Composite module analyst: A fitness-based tool for prediction of transcription regulation

Alexander Kel , Tatiana Konovalova , Tagir Valeev , Evgeny Cheremushkin , Olga Kel-Margoulis and Edgar Wingender


Functionally related genes involved in the same molecular-genetic, biochemical, or physiological process are often regulated coordinately Such regulation is provided by precisely organized binding of a multiplicity of special proteins (transcription factors) to their target sites (cis-elements) in regulatory regions of genes. Cis-element combinations provide a structural basis for the generation of unique patterns of gene expression. Here we present a new approach for defining promoter models based on composition of transcription factor binding sites and their pairs. We utilize a multicomponent fitness function for selection of that promoter model fitting best to the observed gene expression profile. We demonstrate examples of successful application of the fitness function with the help of a genetic algorithm for the analysis of functionally related or co-expressed genes as well as testing on simulated data.

Full Text: PDF

ISBN 3-88579-400-4

Last changed 24.01.2012 21:51:53