Principal biological phenotypes identified as metagenes among TNBC. Heatmaps of expression values of the 16 metagenes (upper panels) and the 355 individual Affymetrix probe sets (lower panels) are shown for the finding cohort (left panels, n = 394) and validation cohort (right panels, n = 185). The dendrogram at the left presents the results from hierarchical clustering of the metagenes. Three major clusters were observed representing (i) basal-like, apocrine, CLDN-CD24, proliferation, and adipocyte metagenes (ii) all five immune cell metagenes, and (iii) the IL-8 and VEGF metagenes, when the hemoglobin and stroma metagenes were left out which display some dataset-bias (see methods). In keeping with these three major phenotypes the samples were sorted according to (1.) Basal-like phenotype, (2.) low vs. high B-Cell metagene, and (3.) the expression value of the IL-8 metagene. (The 355 individual Affymetrix probesets and the respective metagenes are listed in the Additional file 4, Supplementary Methods).