Fig. 3: Tumor microenvironment phenotypes across different calcification groups.

a An overview of gene circuits downregulated in tumors with calcifications of high suspicion for malignancy by mRNA abundance. Nodes represent pathways and edges represent shared genes between pathways. b GSEA showing the downregulated interferon-related pathways within tumors with calcifications of high suspicion for malignancy. c, d The association of mammographic calcifications with the TNBC mRNA subtype (c) and immune subtype (d). “ns” denotes a P-value of > 0.05. e Comparison of the sTILs, iTILs, literature-defined immune signatures, and immunotherapy-response signatures across different calcification groups. f Inferred immune cell infiltrates across tumors with different statuses of calcifications. The center lines represent median values; the bounds of the boxplot represent the interquartile ranges; the whiskers show the range of the data. “***” denotes a P-values of < 0.001; “**” denotes a P-value of < 0.01; “*” denotes a P-values of < 0.05; “ns” denotes a P-value of > 0.05. g Comparison of the expression of PDCD1, CD274, CTLA4, and LAG3 across different calcification groups. “ns” denotes a P-value of > 0.05. The center lines represent median values; the bounds of the boxplot represent the interquartile ranges; the whiskers show the range of the data. All P values were obtained based on logistics regression models with the binomial family used for categorical data (c, d) and the gaussian family used for continuous data (e–g).