Identification of conserved core subnetworks. (a) Representative examples of subnetworks conserved between two organisms. C. jejuni subnetworks are on the left. The top and middle subnetworks (#142 and #307 in Additional data file 6) are conserved with E. coli. The bottom subnetwork (#56) is conserved with yeast S. cerevisiae. Bold lines represent direct interactions, whereas thin lines represent indirect interactions that are direct in the comparison organism (that is, these are predicted interactions). Gene names can be read by zooming in. A complete list of conserved subnetworks between E. coli and S. cerevisiae is available for download at . (b) Hierarchical clustering of the conserved subnetworks. In the clustergram, rows represent proteins and columns represent C. jejuni subnetworks that are conserved with either yeast (left) or E. coli (right). Cores (boxed in red) and modules (boxed in blue) are defined as groups of proteins with similar profiles of subnetwork membership. The cores and modules are enriched for specific functions, for example: Core 1, serine family amino acid metabolism; Module 1-1, serine family amino acid biosynthesis; Module 1-2, generation of precursor metabolites and energy; Module 1-3, oxygen and reactive oxygen species metabolism. Larger versions of this figure are available in the Additional data files, including complex and protein names (Additional data file 8) and a list of function enrichments (Additional data file 9).
Parrish et al. Genome Biology 2007 8:R130 doi:10.1186/gb-2007-8-7-r130