title: Structure-based comparison of four eukaryotic genomes.
abstract: The field of comparative genomics allows us to elucidate the molecular mechanisms necessary for the machinery of an organism by contrasting its genome against those of other organisms. In this paper, we contrast the genome of homo sapiens against C. Elegans, Drosophila melanogaster, and S. cerevisiae to gain insights on what structural domains are present in each organism. Previous work has assessed this using sequence-based homology recognition systems such as Pfam [1] and Interpro [2]. Here, we pursue a structure-based assessment, analyzing genomes according to domains in the SCOP structural domain dictionary. Compared to other eukaryotic genomes, we observe additional domains in the human genome relating to signal transduction, immune response, transport, and certain enzymes. Compared to the metazoan genomes, the yeast genome shows an absence of domains relating to immune response, cell-cell interactions, and cell signaling.
authors.affiliation: Affymetrix, Inc., 6550 Vallejo Street, Emeryville, CA 94608, USA. melissa_cline@affymetrix.com
authors.forename: Melissa
authors.initials: M
authors.lastname: Cline
authors.forename: Guoying
authors.initials: G
authors.lastname: Liu
authors.forename: Ann E
authors.initials: AE
authors.lastname: Loraine
authors.forename: Ronald
authors.initials: R
authors.lastname: Shigeta
authors.forename: Jill
authors.initials: J
authors.lastname: Cheng
authors.forename: Gangwu
authors.initials: G
authors.lastname: Mei
authors.forename: David
authors.initials: D
authors.lastname: Kulp
authors.forename: Michael A
authors.initials: MA
authors.lastname: Siani-Rose
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D003198:Computer Simulation; D004331:Drosophila melanogaster / Q000235:genetics; D004798:Enzymes / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D008957:Models, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D016335:Zinc Fingers / Q000235:genetics
chemical_list: D004798:Enzymes