Genomic gene clustering analysis of pathways in eukaryotes.
Genomic clustering of genes in a pathway is commonly found in prokaryotes due to transcriptional operons, but these are not present in most eukaryotes. Yet, there might be clustering to a lesser extent of pathway members in eukaryotic genomes, that assist coregulation of a set of functionally cooperating genes. We analyzed five sequenced eukaryotic genomes for clustering of genes assigned to the same pathway in the KEGG database. Between 98% and 30% of the analyzed pathways in a genome were found to exhibit significantly higher clustering levels than expected by chance. In descending order by the level of clustering, the genomes studied were Saccharomyces cerevisiae, Homo sapiens, Caenorhabditis elegans, Arabidopsis thaliana, and Drosophila melanogaster. Surprisingly, there is not much agreement between genomes in terms of which pathways are most clustered. Only seven of 69 pathways found in all species were significantly clustered in all five of them. This species-specific pattern of pathway clustering may reflect adaptations or evolutionary events unique to a particular lineage. We note that although operons are common in C. elegans, only 58% of the pathways showed significant clustering, which is less than in human. Virtually all pathways in S. cerevisiae showed significant clustering.
Lee
Jennifer M
JM
Center for Genomics and Bioinformatics, Karolinska Institutet, S171 77 Stockholm, Sweden.
Sonnhammer
Erik L L
EL
D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D017173:Caenorhabditis elegans / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D016000:Cluster Analysis; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D004734:Energy Metabolism / Q000235:genetics; D005057:Eukaryotic Cells / Q000737:chemistry* / Q000378:metabolism*; D005796:Genes / Q000235:genetics*; D005800:Genes, Fungal / Q000235:genetics; D017238:Genes, Helminth / Q000235:genetics; D017344:Genes, Insect / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D016678:Genome; D016681:Genome, Fungal; D015894:Genome, Human; D018745:Genome, Plant; D006801:Humans; D005810:Multigene Family / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics