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Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT

Tom Hiu Cheung1 email, Yin Lam Kwan2 email, Micah Hamady2 email and Xuedong Liu1 email

1Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA

2Department of Computer Science, University of Colorado, 430 UCB, Boulder, Colorado 80309, USA

author email corresponding author email

Genome Biology 2006, 7:R97doi:10.1186/gb-2006-7-10-r97

Published: 25 October 2006

Subject areas: Bioinformatics, Genome studies

Abstract

Deciphering gene regulatory networks requires the systematic identification of functional cis-acting regulatory elements. We present a suite of web-based bioinformatics tools, called GeneACT http://promoter.colorado.edu webcite, that can rapidly detect evolutionarily conserved transcription factor binding sites or microRNA target sites that are either unique or over-represented in differentially expressed genes from DNA microarray data. GeneACT provides graphic visualization and extraction of common regulatory sequence elements in the promoters and 3'-untranslated regions that are conserved across multiple mammalian species.


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