Figure 3
From: Identifying network biomarkers based on protein-protein interactions and expression data
Comparison on pathways enriched by biomarkers identified from PPIA + ellipsoidFN and DEG + ellipsoidFN method. For two biomarker sets identified by the two methods respectively, we used KEGG pathway enrichment search to find several pathways according to their p-values. Then we sort these p-values in ascending order and make a comparison between the two methods on dataset GSE10797 for both two-class and four-class cases. X-axis denotes pathways, while y-axis denotes the p-value of each corresponding pathway. For example, the blue line in the figure on the top shows there are five pathways in total enriched by the node biomarkers whose p-value is lower than 0.1. The small number of pathways that are significantly enriched may result from the fact that there are few genes in the biomarker set and their non-redundant property. From the figure we can easily see that network biomarkers identified by PPIA + ellipsoidFN method tends to enriched to more pathways with lower p-value.