Additional file 5 of Genomic and immune profiling of breast cancer brain metastases

Supplementary Material 5. Differentially expressed genes in matched ECT-BrM specimens. Differentially expressed genes (DEGs) in matched FFPE ECT vs FFPE BrM (n = 8 patients), where log2 fold changes greater than 1 represent higher expression in BrM. DEGs are defined by having an adjusted p-value less than 0.05 and the table includes the top 50 up-regulated and top 50 down-regulated DEGs, sorted by unadjusted p-value. Column names include: Gene symbol, HUGO gene symbol; Base mean, mean of the normalized counts divided by size factors over all samples; Log2 Fold Change, log2 fold change in gene expression; Log2 Fold Change SE, standard error of the log2 fold change; Wald test statistic; P, unadjusted Wald test p value; Adjusted P, FDR adjusted p value; Direction, indicates if the gene is up- or down-regulated with respect to the BrM group.