Fig. 3: Analysis of biological processes associated with gene expression differences between HER2-low and HER2-zero TNBC.
From: Epigenetic determinants of an immune-evasive phenotype in HER2-low triple-negative breast cancer
a The top 10 GO biological processes dysregulated in HER2-low TNBC tumors through GSEA. Pathways are sorted by NES (x-axis). b The top 10 molecular pathways associated with genes downregulated in HER2-low TNBC. The ratio (x-axis) represents the proportion of genes downregulated per total number of genes in the pathway. c Cascade plot representing differential gene expression of HLA genes between HER2-low and HER2-zero TNBC tumors in the TCGA cohort. The red color illustrates statistical significance. Wald test from the DESeq2 pipeline was used to assess statistical differences, P < 0.05. d Upset plot showing the immune-related pathways assessed using GSEA that are exclusively or commonly significant across TCGA (n = 411) and the validation datasets I-SPY2 (n = 182) and SCAN-B (n = 11) between HER2-low and HER2-zero TNBC tumors. The intersections indicate the number of pathways shared among the respective datasets. TNBC triple-negative breast cancer, GO gene ontology, GSEA gene set enrichment analysis, NES normalized enrichment score, HLA human leukocyte antigen.
