Figure 3

Gene expression from tumor-infiltrating stromal and immune cells contributes to the expression space. (A) ESTIMATE scores for each of the four groups of samples, where a higher score indicates a higher proportion of hNTI cells. (B) Gene expression space using the same samples as in Figure 2A, but excluding genes from the hNTI cell signature. See correlation plot between ESTIMATE score and Y-axis from Figure S7B in Additional file1. (C) Gene expression space defined after in silico correction of the hNTI cell effect. The coordinates in each axis correspond to the residuals of the linear regression fits of each MCA component in (B) (see Materials and methods for details). Complementary analyses with the same samples as in Figure 2A, but using only genes from the hNTI cell signature, are shown in Figure S7 in Additional file1. Complementary analyses using cell lines are shown in Figures S8 and S9 in Additional file1.