Figure 5

An eye relevant network identified with the pmax expression filter. The DroID database was searched for protein interactions involving genes in the KEGG pathway for phototransduction. The network was then filtered to remove genes expressed in the eye below 45% of their maximal value (pmax). The resulting network has 498 interactions among 351 proteins, including 15 of the KEGG pathway phototransduction proteins (squares) and 55 proteins encoded by genes known to have eye-related mutant phenotypes (see text). Among the proteins encoded by genes with eye-related phenotypes, 32 had tissue expression data (dark blue) and thus were subject to the pmax filter, while 23 had no expression data (light blue). After the initial analysis of phenotypes, examination of updated gene annotations and literature revealed an additional two genes with functions related to phototransduction (red). Edge colors reflect the source of the protein interaction data as described in Methods: dark green and yellow are human and C. elegans interologs, respectively; light blue and pink are from large co-complex studies; dark blue, green, and dark grey are from three separate large scale two-hybrid studies; orange are from literature databases; red are from more than one source. The pmax filter was set by default to retain genes that had no expression data. Deletion of genes with no expression data would result in a network further enriched for genes with eye related phenotypes, from 16.7% (58/348) to 20.3% (28/138); however, it would also eliminate many eye relevant genes, including genes with known eye related phenotypes that would no longer be connected to the network just because their expression is currently unknown.