PenDA, a rank-based method for personalized differential analysis: Application to lung cancer
Fig 7
Upregulation of 37 genes in adenocarcinoma is a strong predictor of poor prognosis.
(a) Principal Component Analysis on ADC cohort. Each cross represents an individual sample. The color of the dots represents the three subclasses defined in Fig 6. (b) Survival of ADC patients classified according to the 2 main subtypes (classes II and III). (c) The percentage of deregulated patients within the ADC class II (y-axis) or the ADC class III (x-axis). Each dot corresponds to one gene. The contour lines correspond to the density of genes. Pink dots indicate genes with a significant higher proportion of deregulation in the class II (proportion test, p-value < 0.05 after Bonferroni correction for multiple testing). Red dots define 37 genes highly deregulated (>75%) in the class II group and lowly deregulated (<25%) in the class III group. (d) (Top) Classification of ADC TCGA-LUAD built on the total number of up-regulated genes among the subset of 37 classifiers defined in (c). Patients are separated into 3 discrete groups: a group with a low upregulation (black, score < 4), a group with intermediate deregulation (gray, 4 ≤ score < 34) and a group with most genes upregulated (red, 34 ≤ score). (Bottom) Survival of patients according to these 3 groups. (e) As in (d) but for ADC Grenoble Hospital patients. Patients are separated into 3 discrete groups: a group with a low upregulation (black, score ≤ 0), a group with intermediate deregulation (gray, 0 < score < 15) and a group with most genes upregulated (red, 15 ≤ score).