title: oPOSSUM: integrated tools for analysis of regulatory motif over-representation.
abstract: The identification of over-represented transcription factor binding sites from sets of co-expressed genes provides insights into the mechanisms of regulation for diverse biological contexts. oPOSSUM, an internet-based system for such studies of regulation, has been improved and expanded in this new release. New features include a worm-specific version for investigating binding sites conserved between Caenorhabditis elegans and C. briggsae, as well as a yeast-specific version for the analysis of co-expressed sets of Saccharomyces cerevisiae genes. The human and mouse applications feature improvements in ortholog mapping, sequence alignments and the delineation of multiple alternative promoters. oPOSSUM2, introduced for the analysis of over-represented combinations of motifs in human and mouse genes, has been integrated with the original oPOSSUM system. Analysis using user-defined background gene sets is now supported. The transcription factor binding site models have been updated to include new profiles from the JASPAR database. oPOSSUM is available at http://www.cisreg.ca/oPOSSUM/
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver BC, Canada.
authors.forename: Shannan J
authors.initials: SJ
authors.lastname: Ho Sui
authors.forename: Debra L
authors.initials: DL
authors.lastname: Fulton
authors.forename: David J
authors.initials: DJ
authors.lastname: Arenillas
authors.forename: Andrew T
authors.initials: AT
authors.lastname: Kwon
authors.forename: Wyeth W
authors.initials: WW
authors.lastname: Wasserman
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D051379:Mice; D016328:NF-kappa B / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D016328:NF-kappa B; D014157:Transcription Factors