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

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

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.