Article |
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm
1 A.P. Ershov's Institute of Informatics Systems 6, Lavrentiev avenue, 630090 Novosibirsk, Russia 2 Institute of Cytology and Genetics Novosibirsk, Russia 3 BIOBASE GmbH Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany 4 Department Bioinformatics, UKG/University Göttingen Goldschmidtstr. 1, D-37077 Göttingen, Germany
*To whom correspondence should be addressed. Tel: +49-5331-858441; Fax: +49-5331-858470; Email: alexander.kel{at}biobase-international.com
Received February 15, 2006. Revised March 4, 2006. Accepted April 18, 2006.
Composite Module Analyst (CMA) is a novel software tool aiming to identify promoter-enhancer models based on the composition of transcription factor (TF) binding sites and their pairs. CMA is closely interconnected with the TRANSFAC® database. In particular, CMA uses the positional weight matrix (PWM) library collected in TRANSFAC® and therefore provides the possibility to search for a large variety of different TF binding sites. We model the structure of the long gene regulatory regions by a Boolean function that joins several local modules, each consisting of co-localized TF binding sites. Having as an input a set of co-regulated genes, CMA builds the promoter model and optimizes the parameters of the model automatically by applying a genetic-regression algorithm. We use a multicomponent fitness function of the algorithm which includes several statistical criteria in a weighted linear function. We show examples of successful application of CMA to a microarray data on transcription profiling of TNF-alpha stimulated primary human endothelial cells. The CMA web server is freely accessible at http://www.gene-regulation.com/pub/programs/cma/CMA.html. An advanced version of CMA is also a part of the commercial system ExPlainTM (www.biobase.de) designed for causal analysis of gene expression data.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Walczak-Drzewiecka, M. Ratajewski, W. Wagner, and J. Dastych HIF-1{alpha} Is Up-Regulated in Activated Mast Cells by a Process That Involves Calcineurin and NFAT J. Immunol., August 1, 2008; 181(3): 1665 - 1672. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Wingender The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation Brief Bioinform, July 1, 2008; 9(4): 326 - 332. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Abascal, P. Carmona-Saez, J.-M. Carazo, and A. Pascual-Montano ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data Bioinformatics, May 1, 2008; 24(9): 1208 - 1209. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Cordero, M. Botta, and R. A. Calogero Microarray data analysis and mining approaches Brief Funct Genomic Proteomic, January 22, 2008; (2008) elm034v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Papatsenko ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors Bioinformatics, April 15, 2007; 23(8): 1032 - 1034. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. J. Donaldson and B. Gottgens CoMoDis: composite motif discovery in mammalian genomes Nucleic Acids Res., January 12, 2007; 35(1): e1 - e1. [Abstract] [Full Text] [PDF]
|
|