Serial gene and protein expression of example subnetwork genes during disease progression. (A) Gene expression changes in serial samples of 30 additional patients registered at UC San Diego. Rows and columns represent genes and patients, respectively. The color of each block scales with the log2-transformed ratio of a gene in the earlier sample (SC1) compared with the later sample (SC2) of a particular patient. Both SC1 and SC2 are before TX. The “average” rows illustrate the averaged expression change of genes in similar subnetworks across patients. Genes participating in similar subnetworks are clustered together and the figures of the corresponding subnetworks are indexed next to each cluster. Patients are clustered based on their changes on gene expression by a hierarchical clustering dendrogram. (B) Survival analyses on SC2→TX are shown for both cluster 1 (red line) and cluster 2 (green line) segregated by gene expression changes in panel A. (C) Heatmap of protein expression changes of MYC and TNFRSF7 measured by flow cytometry in serial samples of 16 patients registered at UC San Diego. Colors represent the percentage of change in median florescence intensity of a protein in the later sample compared with the earlier sample of a particular patient. (D) Immunoblotting of MYC, SMAD2, and CCT4 in serial samples of 5 patients.