cis-Regulatory Element Prediction in Mammalian Genomes

The identification of cis-regulatory elements and modules is an important step in understanding the regulation of genes. We have developed a pipeline capable of running multiple motif prediction methods on a whole genome scale. Using gene expression datasets to identify coexpressed genes and the Ensembl Compara database orthologues, we assemble input sequence sets comprised of the upstream regions of a target gene, its orthologues and co-expressed genes on the premise that such genes will share promoters by evolution (orthologues) or share regulatory control mechanisms (co-expressed genes). Co-expressed genes are identified by an approach that combines Pearson distances from multiple gene expression datasets derived from multiple experimental approaches and calibrated against the GO database. Our pipeline runs a number of established motif detection algorithms with a range of parameter settings on the input dataset. We integrate the diverse result sets by scoring motifs with a method-...

• Type: Conference
• Year: 2005
• Where: CSB
• Authors: Asim S. Siddiqui, Gordon Robertson, Misha Bilenky, Tamara Astakhova, Obi L. Griffith, Maik Hassel, Keven Lin, Stephen Montgomery, Mehrdad Oveisi, Erin Pleasance, Neil Robertson, Monica C. Sleumer, Kevin Teague, Richard Varhol, Maggie Zhang, Steven J. M. Jones
• Keywords: Bioinformatics, Co-expressed Genes, CSB 2005, Gene Expression Datasets, Target Gene