PMC5871915_01
Network-based analysis of highly mutated pathways of 31 cancer types in TCGA data. The highly mutated pathways detected by a network-based analysis and b standard enrichment analysis. The pathways of interest in the discussion are highlighted in blue, and the pathways only enriched by network-based analysis are highlighted in red
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Fig5
Fig. 5. For the analysis, the mutation frequencies among the patients in the 31 TCGA provisional studies were downloaded from cBioPortal for Cancer Genomics. This network-based analysis clearly detects more significantly mutated pathways than the analysis without using the network, as shown in Fig. 5a, b, respectively.  Interestingly, the network-based analysis in Fig. 5a indicates that the AMPK signaling pathway is affected in breast cancer (BRCA) and uterine corpus endometrial cancer (UCEC).
Network-based analysis of patient mutation data in TCGA ovarian cancer. The significantly mutated pathways in each patient detected by a network analysis and b the analysis of the original mutation data without the network. c The survival plot of the three groups detected by the network-based pathway analysis of the TCGA ovarian cancer patients. Derived by standard log-rank test, the p-values for comparing group 2 vs. group 3 and group 1 + group 2 vs. group 3 are both significant. d The survival plot of the groups detected by the analysis of the original mutation data of the TCGA ovarian cancer patients
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Fig6
In the case study on the ovarian cancer patients shown in Fig. 6, the mutation data of the 316 TCGA ovarian cancer patients were downloaded from the Xena Public Data Hubs. The network-based analysis informs a clustering of the patients by a significant relevance to survival (Fig. 6c). Notably, three subgroups of tumor samples can be identified from the network-based analysis shown in Fig. 6c, compared to four subgroups in the mutation-based analysis without the network in Fig. 6d.