Fig. 3

Topological and functional analysis of the weighted correlation networks. A Heat map for JI values for comparing the communities of stage I-specific network with the communities of other stages. The color-scale is from white for the minimum value of JI (0%) to green for the maximum value (36%). The largest value in each table is selected to perform the functional enrichment. B Functional comparison of the KEGG pathways with p-values ≤ 0.01 and having more than 10 genes for the third community of stage I-specific network with the corresponding communities of other stages. The third community of stage I is very similar to the first community of stage II in terms of the gene counts and p-values of the enriched pathways but less similar to the second community of normal, stages III and IV. C Functional comparison (edge-based enrichment) of the stage-specific and stage-unique networks for 24 cancer-related pathways. The pathways are divided into five categories: cancer related, cell cycle/proliferation/growth, inflammation, angiogenesis and metastasis. Functional enrichment is carried out for both “stage-specific” and “stage-unique” networks. Number of edges related to the genes enriched in each pathway are indicated by the size of the dots. Color scale of the dots indicate p-value with a cut-off of 0.05. D Connectivity of p53 signaling pathway genes across different stage-unique networks. The nodes are colored based on the log2FC values (in a specific stage vs. normal) across the four stages I-IV (dark blue (log2FC of -2) to white (0) to dark red (2)). Each node represents four log2FC values, going from left to right. Edges are colored differently across stages as follows: green for edges in stage I, cyan in stage II, yellow in stage III, and purple in stage IV. E Connectivity of p53 signaling pathway genes in normal