FIGURE 3 from Stromal Signals Dominate Gene Expression Signature Scores That Aim to Describe Cancer Cell–intrinsic Stemness or Mesenchymality Characteristics

Comparison of EMT-related gene expression signature scores in tumor and normal tissue that is adjacent to the tumor tissue. Tumor samples are separated into low, medium, and high cancer cell content (CPE) based on the 25th (low) and 75th (high) percentiles of TCGA cancer cell content estimates. Lines indicate the paired tumor (T) and normal adjacent to tumor (NAT) samples. Colors indicate the cancer cell content in tumor samples with low (blue), or high (red) cell content or gray for missing data. Scores in NAT and high cancer cell content samples were compared using one-sided paired t tests for the “T high” and NAT comparison and a one-sided t test for the “T high” versus “T low” comparisons. P values were adjusted using Bonferroni correction (0 = ****, <1e-4 = ***, <0.001 = **, <0.05 = *, ns).