Protein Networks as Logic Functions in Development and Cancer
Figure 3
Network modules capture causal developmental factors and are reproducible.
(A) Consensus network modules underlying tissue origin (modules of size greater than 2 are encircled). Gene pairs that often co-occur in the same decision trees and are most important for classification are shown in blue. Node color indicates protein importance whereas edge width indicates the importance of a protein combination. (B) Enrichment for developmentally-related phenotype categories in the MGI database (FDR is reported above each bar). (C) Enrichment of germ-layer specific genes identified by NGF based on the Gene Ontology (FDR is reported above each bar). (D) Percentage of genes, interactions, and modules that were reproduced based on an independent dataset. (E) Percent of reproduced single genes and gene combinations (Fisher's Exact Test P-values are reported). NGF* indicates the result for NGF applied to networks with perturbed expression measurements.