Additional file 7 of Genomic and immune profiling of breast cancer brain metastases

Supplementary Material 7. Gene set enrichment analysis results based on pathways of interest in matched ECT-BrM specimens. Results of gene set enrichment analysis (GSEA) based on selected pathways of interest (MNK, CDK, DNA damage repair, immune signaling, oxidative phosphorylation) from HALLMARK, KEGG, and GO gene lists and literature were compared in matched FFPE ECT-FFPE BrM specimens (n = 8 patients), ranked by unadjusted p value. Column names include: Pathway type, biologically-relevant pathway group name; Pathway, unique pathway identifier; P, unadjusted enrichment p value; Adjusted P, FDR adjusted p value; ES, enrichment score; NES, enrichment score normalized to mean enrichment of random samples of the same size; Number of genes, number of genes analyzed in the pathway; leadingEdge, HUGO gene symbols of leading-edge genes.