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

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

Author Affiliations

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

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

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Genome Biology 2006, 7:R97  doi:10.1186/gb-2006-7-10-r97

Published: 25 October 2006

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.