Gene set enrichment results for ER-negative breast cancers. Running enrichment scores (RES) and the location of each probe set within the complete ranked ordered gene list for each gene set. The first dotted line indicates the position of the maximum RES, the second dotted line indicates the zero position of the ranking metric score. A, proliferation set (probe set n = 74). B, genomic grade index (probe set n = 242). C, E2F3 pathway (probe set n = 173) (pCR = pathologic complete response; RD = residual disease). Heat maps corresponding to these plots are provided on supplementary figure 1 in Additional file 2.