Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals.
BACKGROUND
Given genetic networks derived from two genomes, it may be difficult to decide if their local structures are similar enough in both genomes to infer some ancestral configuration or some conserved functional relationships. Current methods all depend on searching for identical substructures.


METHODS
We explore a generalized vertex proximity criterion, and present analytic and probability results for the comparison of random lattice networks.


RESULTS
We apply this criterion to the comparison of the genetic networks of two evolutionarily divergent yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, derived using the Synthetic Genetic Array screen. We show that the overlapping parts of the networks of the two yeasts share a common structure beyond the shared edges. This may be due to their conservation of redundant pathways containing many synthetic lethal pairs of genes.


CONCLUSIONS
Detecting the shared generalized adjacency clusters in the genetic networks of the two yeasts show that this analytical construct can be a useful tool in probing conserved network structure across divergent genomes.
Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada K1N 6N5.
Zhenyu
Z
Yang
David
D
Sankoff
D000465:Algorithms; D017124:Conserved Sequence; D053263:Gene Regulatory Networks; D005804:Genes, Lethal; D016681:Genome, Fungal; D008957:Models, Genetic; D005810:Multigene Family; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012568:Schizosaccharomyces / Q000235:genetics*