Figure 2

(a) Combined analysis of the association between PTEN SCNA status and differential gene expression of PTEN for all 30 tumors in the Pan-cancer cohort. Boxplots show the relationship between PTEN normalized transcript counts Log² (Y-axis) versus PTEN SCNA status (HemDel, HomDel, Dupl and Intact). The mean transcript count for PTEN intact was 18.78, HomDel was the lowest expression level at 17.15, and HemDel showed reduced expression at 18.26, but Dupl was slightly higher than intact at 19.20. The mean transcript counts for all three classes of SCNA significantly deviated from intact (P < 0.0001, t-test). (b) Association between PTEN SCNA status and differential gene expression of PTEN for the 23 most common solid tumors in the Pan-cancer cohort. Boxplots show the relationship between PTEN transcript counts Log² (Y-axis) versus PTEN SCNA status HomDel (red), HemDel (blue), and Intact (green) for each tumor. For most of tumors, the mean transcript counts for both HomDel and HemDel deviated significantly from intact (P < 0.05). Plotted using ggplot2 (https://ggplot2.tidyverse.org/).