Fig. 3: Recurrence in FinXX and Mayo Clinic TNBC_TMA cohorts as a function of PD-L1 protein abundance and the APC or TCA eigenprotein scores.

Each dot or square represents tumor-average values for each feature in each tumor, including tumors that recurred (yellow squares) and tumors that did not recur (blue circles). The X axis contains numerical scores for the APC or TCA eigenproteins, and the Y axis contains PD-L1 protein log2 normalized counts for intraepithelial segments. Odds ratios (ORs) for 5-year recurrence were calculated as dichotomous variables (recurrence YES or NO). The reference lines indicate the population median values for each feature, and ORs were calculated in reference to samples that were <median for both features (e.g., APClow/TCAlow). Significance was defined as p < 0.05, and “quadrants” with p > 0.05 for ORs are designated as “ORns”. ORs for FinXX APClow/TCAhigh and APChigh/TCAlow are not given in Fig. 3, considering the low number of samples in these quadrants. However, ORs for all quadrants are given in Supplementary Table 3. Source data are given in Supplementary Data 2 (FinXX tumor-average abundance), Supplementary Data 7 (TNBC_TMA), and Supplementary Data 5 (eigenprotein scores). Patient numbers: FinXX, 22 recurred and 22 did not recur; TNBC_TMA, 81 recurred and 181 did not recur.