Gene expression profiles of T cells. Gene expression profiles of T cells. In all panels, NP and P indicate normal breast of nulliparous and parous women, respectively. A, 3-D Principal Component Analysis plot of RNA-seq data. B, Heat map depicting clustering of samples based on the expression of top differentially expressed immune-related genes with highest variance defined by both edgeR and DESeq2. C, Frequency of enrichment of a particular cell type following GSEA using the Immune c7 compendium. Significance was determined using proportionality test with multiple testing correction. *, P < 0.05 after correcting for multiple hypothesis testing. D, Network of enriched immune c7 cell type–specific gene sets. Node size is reflective of number of times a T-cell type appears as significantly enriched, and arrow thickness is reflective of number of significant gene sets involved in a particular comparison. E, Frequency of T-cell populations calculated using CIBERSORT based on RNA-seq expression data from bulk T-cell samples, with difference in populations computed using ANOVA. Carlos R. Gil Del Alcazar et al. Cancer Discov 2017;7:1098-1115 ©2017 by American Association for Cancer Research