Figure 1

Expression of PD-1 (PDCD1) and PD-L1 (CD274) mRNA within tumor samples correlates with a type 1 immune gene signature. Principal coordinate analysis was applied to expression data for a subset of immune-related genes obtained from the invasive breast cancer arm of the Cancer Genome Atlas (Figure S3 in [4]). Biplot projections of the genes along the first two principal coordinate directions, where principal coordinate 1 corresponds to a type 1 immune signature and principal coordinate 2 corresponds to oncogenic transformation in invasive breast cancer. Type 1 immune related genes are shown in black in (A) while immunosuppressive genes are highlighted in (B). The first two principal coordinates capture 33% of the overall variance in the data. As principal coordinates are independent, the projection of a gene along the corresponding axes indicates the degree to which the expression of two genes are related and the distance from the origin indicates the strength of the covariation within the data set. The remaining principal coordinates capture progressively less variance in the data and provide little additional information. The colored ovals radiating out from the origin indicate principal coordinate values that cannot be distinguished from random noise, that is, a null hypothesis, with increasing levels of statistical stringency. These colored ovals were obtained by bootstrap resampling.