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.

补充文件9：表S2。DTBC与LumA型肿瘤的差异突变及体细胞拷贝数变异（Somatic Copy Number Alterations, SCNA）。（A）DTBC与LumA型肿瘤相比，存在显著差异（p值<0.1）的非同义体细胞短变异（单核苷酸变异（Single Nucleotide Variant, SNV）与插入缺失（Insertion-Deletion, INDEL））相关突变基因。本部分报告了弗斯逻辑回归的比值比与p值。（B）染色体臂水平的体细胞拷贝数变异（SCNA）在DTBC与LumA型肿瘤间存在显著差异（p<0.05）。变异值≥0.1的样本被归类为扩增，≤-0.1的样本被归类为缺失。表格的排序与图2D的聚类排布一致。（C）与局灶性SCNA峰相关的基因在DTBC与LumA型肿瘤间存在显著差异（错误发现率（False Discovery Rate, FDR）<0.05）。相对SCNA≥0.1的样本被归类为扩增，≤-0.1的样本被归类为缺失。本表格提供了基因SCNA与RNA表达的威尔科克森检验p值、校正后p值以及皮尔逊相关系数（r）。表格按照细胞遗传学条带、起始坐标及FDR校正p值进行排序。表格中标注了与细胞增殖相关的基因。