Figure 4

Nitrate reductase subnetwork. We show a small cluster that is present in the runs-informed network and absent in the unweighted hypergeometric network that does not use runs. The phylogenetic profiles of the corresponding genes are shown in (a). Significant edges are shown in (b) with blue edges being identified by both methods while green edges belong only to the runs-informed network. We note that the only elements of this network detected by the non-runs-using method are two highly homologous nitrate reductase complex subunits; the other members are less homologous and are missed by it. Even though these genes occur in relatively few genomes, those in which they occur are widely scattered and form many runs in the profiles, leading to their correct inclusion in the runs-informed network.