Fig. 11.

Comparison of APE1 and NPM1 gene expression levels and functional characterization of APE1/NPM1 correlated genes. Scatter plot showing the relationship existing between APE1 and NPM1 expression levels in TCGA Breast Invasive Carcinoma patients (n = 1105). The red dash-dotted lines represent the first and third quartile fits, the central dashed line represents the mean smooth and the green line represents the fitted regression line (Ordinary Least Squares). Marginal boxplots are also shown (a). Two lists of genes with APE1/NPM1 correlated expression (ρs ≥ + 0.5 or ρs ≤ − 0.5, p ≤ 0.05) were identified in two groups of TNBC patients having an OS higher (b, n = 44) or lower (c, n = 23) than 5 years. Functionally enriched terms (Benjamini-Hochberg adjusted p ≤ 0.05) were identified using the Cytoscape plugin ClueGO, querying several functional and metabolic databases, and results were summarized as pie charts. The same analysis was repeated on a group of patients (n = 23) that had a relapse of the disease after at least one year from diagnosis, analyzing separately the gene signatures with positive (ρs ≥ + 0.5, p ≤ 0.05, n = 54) or negative (ρs ≤ − 0.5, p ≤ 0.05, n = 61) correlation with APE1/NPM1 (d, e)