PenDA, a rank-based method for personalized differential analysis: Application to lung cancer
Fig 5
The gene deregulation pattern.
(a-b) Scatterplots of the percentage of up-regulated versus down-regulated patients in the ADC (left panel) and SQCC (right panel) cohorts. Each dot corresponds to one gene. The x-axis indicates the percentage of up-regulation within the cohort, the y-axis indicates the percentage of down-regulation within the cohort. The contour lines correspond to the density of genes. Genes that are significantly differentially expressed at the individual level (t-statistic, q-value < 0.05) are represented using the following color code: green genes are super-conserved (SC), blue genes are super-down-regulated (SD), red genes are super-up-regulated (SU), other genes are depicted in gray. (C) Venn diagrams indicating the total number of SC, SU and SD genes in ADC and SQCC cohorts. (d-e-f) (Top panels) Distributions of gene expression levels (normalized counts) for three representative genes (the SC gene CAPS in (d), the SU gene ESPRP1 in (e), the SD gene RILPL2 in (f)) in the ADC cohort (yellow), in the SQCC cohort (purple), and for the control patients (gray). The dashed lines represent the mean expressions. (Bottom panels) The corresponding percentages of patients deregulated for each shown gene in ADC and SQCC cohorts are represented by bar plots: gray for non-deregulated patients, blue for down-regulated patients and red for up-regulation patients.