Significance rank of breast cancer pathways tested by both GBJ and GSEA.

The significance ranking of pathways according to GBJ and GSEA, colored according to density of SNPs with p < 10−5. Pathways are ordered according to p-value (GBJ) or q-value (GSEA), smaller rankings indicate more significance. For the sake of presentation, we only show pathways in the top ten percentiles of either GSEA or GBJ as well as pathways in the 30th-40th and 60th-70th percentiles of GBJ. Pathways ranked by GBJ as more significant generally have a higher proportion of SNPs with p < 10−5. In contrast, there is no discernible relationship between a pathway’s GSEA ranking and its density of suggestive signals.