Extended Data Figure 10. Network analysis of the subtype signature proteins.

a, The number of signature proteins for each subtype. For a given subtype, the red circle represents proteins that were different in abundance between the subtype and all other subtypes, the green circle represents proteins that were different in abundance between the subtype and normal colon tissues. The intersection between red and green circles contains the signature proteins for each subtype. b, Visualizing subtype C signature proteins in NetGestalt. Proteins in the iRef protein-protein interaction network are placed in a linear order together with the hierarchical modular organization of the network. Alternating bar colors (green and orange) are used to distinguish neighboring modules. Proteins in the up- and down-signatures of subtype C were visualized as two separate tracks below the network modules, where each bar represents a protein. These proteins are not randomly distributed in the network. Highlighted by red or blue arrows are four Network modules (I, IV, V, VI) significantly enriched with up-signature proteins and two modules (II and III) significantly enriched with down-signature proteins (adjusted p value < 0.01). c–d, Heat maps depicting relative abundance of down- and up-signature proteins of subtype C in modules III and I, respectively. Tumors are displayed as rows, grouped by normal controls (N) and proteomic subtypes (A–E) as indicated by different side bar colors. Proteins are displayed as columns. e–f, Network diagrams depicting the interaction of down- and up-signature proteins of subtype C in modules III and I, respectively. Node and node-border colors represent relatively higher or lower abundance in the subtype compared to other subtypes and normal colon tissues, respectively. Red and blue in the heat maps and the network diagrams represent relatively higher or lower abundance, respectively.