Additional file 9 of Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Additional file 9. Table S2. Differential mutations and SCNA between DTBC and LumA tumors. (A) Significantly (p-value < 0.1) differentially mutated genes with non-synonymous somatic short variants (SNV and INDEL) in DTBC versus LumA tumors. Odds ratio and p-value of the Firth logistic regression are reported. (B) Somatic copy number alterations (SCNAs) at the chromosome arm level that show significant differences (p < 0.05) between DTBC and LumA tumors. Samples with a value of > = 0.1 were classified as amplified, and those with < = − 0.1 were categorized as deleted. The table’s order corresponds to the clustering arrangement of Fig. 2D. (C) Genes linked with focal SCNA peaks displaying significant differences (FDR < 0.05) between DTBC and LumA tumors. Cases with a relative SCNA of > = 0.1 are categorized as amplified, while those with < = − 0.1 are classified as deleted. The table provides Wilcoxon test p-values, adjusted p-values, and Pearson’s correlation coefficient (r) for gene’s SCNA and RNA expression. The table is arranged by cytoband, start coordinate, and FDR-adjusted p-values. Genes associated with cell proliferation are indicated in the table.