Figure 3

Empirical survey and performance evaluation of DE-based network strategy. (a) The known influenza host resistance genes are surrounded by differentially expressed genes between resistant and susceptible mouse strains. To visualize the gene expression levels within a network context, a sub-network consisting of only the seed genes and their directly linked neighbors in the STRING database was extracted and visualized using Cytoscape[34] under the edge-weighed spring embedded layout. The distances between seeds and their neighbors were set proportional to their interaction scores. Differential expression levels between resistance and susceptible mouse strains are mapped to the size and color shade of each node. The significant differentially expressed genes were highlighted by unifying the colors of genes with DE levels that ranked at the top 5% (DE level ≥ 0.32) among the whole genome in red and the genes with DE levels that ranked at the bottom 5% (DE level ≤ -0.15) in blue (as illustrated in the inset). All seed genes are highlighted using the same node size and bold fonts of their names. (b) The ROC curves of DE-based methods in the validation test on known host resistance genes. Three methods (DER, DNR, and deHKDR) as described in the main text were compared. The performance measured as AUC is shown next to the name of each method.