Serial expression of example subnetwork genes and the subnetwork signature along disease progression. (A) Subnetwork activities in serial samples of 9 additional patients registered at UC San Diego. Rows and columns represent subnetworks and patients, respectively. SC1 marks the earlier sample while SC2 represents the later sample of the same patient. Both SC1 and SC2 are before TX. The color of each block scales with the activity level of a subnetwork in a particular patient at either SC1 or SC2 relative to the average activity of all the studied samples. The static factor status of patients is listed above the columns: “A” indicates unmated IGHV and ZAP70 positive; and “B”, mutated IGHV and ZAP70 negative. (B) Subnetwork activity changes in serial samples of 13 patients from Fernandez and colleagues.¹⁰  Rows and columns represent subnetworks and patients, respectively. The color of each block scales with the activity change in a subnetwork from the initial versus subsequent sample of each particular patient. The heatmap of patient F9 is separately displayed because of its contrasting pattern versus the other 12 patients. The average change column illustrates the averaged activity change in a subnetwork across patients: the column with an asterik (*) represents the average of all the 13 patients, whereas the column labeled “average change” without the asterisk excludes the data from patient 9. The rightmost column denotes the prognosis power of the 38 subnetworks on UC San Diego samples (the coefficient of each subnetwork as the predictor in a univariate Cox hazard model on SC→TX). The subnetworks that have significant differences between initial and subsequent samples from each patient in Fernandez and colleagues¹⁰  (P < .05 from a 1-tailed t test) are indicated by the figure panels in which they are displayed (“3C”, “3I”, etc).