Genomic gene clustering analysis of pathways in eukaryotes.

By Jennifer M. Lee, Erik L. L. Sonnhammer. Genome Research, 2003

341 citations recorded by the source corpus.

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.

Subfields: Aging, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6a836ed6d27b421a85ab3e7b03ebfb24e7a978cf

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Walking the interactome for prioritization of candidate disease genes. (2008, background): “For instance, genes in the same metabolic pathway show statistically significant genomic clustering as compared to randomly chosen genes.(34) Additionally, we found that proteins coded by genes in the contiguous intervals around disease genes are located in greater proximity to the corresponding dis”
Mating-Type Structure, Evolution, and Function in Euascomycetes (2006, background): “Moreover, the nature of gene clusters in the MAT environment might reveal new pathways involved in the sexual process, since there is growing evidence that co-regulated genes may be found clustered in fungal genomes (Lee and Sonnhammer 2003).”
Taverna: a tool for the composition and enactment of bioinformatics workflows (2004, background): “Obtaining information about the metabolic or signalling pathways associated with a gene product is an analysis which is commonly performed in bioinformatics (Yanai et al., 2002; Lee and Sonnhammer, 2003; Hannenhalli and Levy, 2003).”
The evolutionary dynamics of eukaryotic gene order (2004, background): “We can now, for example, ask whether there are more metabolic pathways in which two or more genes are clustered than would be expected by chanc”
Advanced Heat Map and Clustering Analysis Using Heatmap3 (2014, background): “When applied to both, the heat map can help visualizing potential novel pathways [5] and coexpression patterns [6].”
Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution (2004, background): “Although some degree of functional clustering of genes is observed in the Arabidopsis genome (Elo et al., 2003; Lee and Sonnhammer, 2003), genes involved in the same pathway are usually scattered, so smallscale DNA duplications cannot simultaneously duplicate all the components of a pathway.”