Figure 2
(A). ncNAT and PCT transcript distributions in adjacent non-malignant healthy tissue and tumors. Density plot of log10 (mean counts) of the four transcript types (ncNAT tumor; ncNAT non-malignant, PCT tumor, PCT non-malignant). The upper panel contains the complete list of 9632 ncNAT/PCT pairs; the second panel contains ncNAT/PCT pairs in amplified genomic regions; the third panel contains ncNAT/PCT pairs in deleted genomic regions; and the last panel contains ncNAT/PCT pairs in copy-number-neutral genomic regions. The ncNAT distributions are clearly different in non-malignant and tumor tissues, with a higher number of ncNATs displaying reduced expression in the tumors than the number of ncNATs that are increased in the tumors. (B) Presents the same information as panel A, but in the highly expressed ncNAT subgroup of the 4882 ncNAT/PCT pairs. (C) Schematic representation of proportion of different classes of differential correlations between tumors and non-malignant tissues. Primarily positive correlations of expression between ncNAT and their corresponding PCT are created or lost in tumorous tissues. The numbers indicated in the graph are the number of ncNAT/PCT pairs in this category; +/+= significant positive correlation between ncNAT and PCT in adjacent non-malignant tissue and conserved in the tumor; +/−= significant positive correlation between ncNAT and PCT in the adjacent non-malignant tissue that becomes negative in the tumor; +/0= significant positive correlation between ncNAT and PCT in the adjacent non-malignant tissue that is lost in the tumor; −/−= significant negative correlation between ncNAT and PCT in adjacent non-malignant tissue that is conserved in the tumor; −/+= significant negative correlation between ncNAT and PCT exists in adjacent non-malignant tissue that becomes positive in the tumor; −/0= significant negative correlation between ncNAT and PCT in the adjacent non-malignant tissue that is lost in the tumor; 0/0 = no significant correlation between ncNAT and PCT exists in the adjacent non-malignant tissue or the tumor.
