More robust detection of motifs in coexpressed genes by using phylogenetic information

Background: Several motif detection algorithms have been developed to discover overrepresented motifs in sets of coexpressed genes. However, in a noisy gene list, the number of genes containing the motif versus the number lacking the motif might not be sufficiently high to allow detection by classical motif detection tools. To still recover motifs which are not significantly enriched but still present, we developed a procedure in which we use phylogenetic footprinting to first delineate all potential motifs in each gene. Then we mutually compare all detected motifs and identify the ones that are shared by at least a few genes in the data set as potential candidates. Results: We applied our methodology to a compiled test data set containing known regulatory motifs and to two biological data sets derived from genome wide expression studies. By executing four consecutive steps of 1) identifying conserved regions in orthologous intergenic regions, 2) aligning these conserved regions, 3) c...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Pieter Monsieurs, Gert Thijs, Abeer A. Fadda, Sigrid C. J. De Keersmaecker, Jozef Vanderleyden, Bart De Moor, Kathleen Marchal
• Keywords: BMCBI 2006, Motif Detection, Regulatory Motifs, Several Motif Detection