Cluster 3 showed significant differential methylation at 149 CpGs in 116 genes compared with all other breast tumors after accounting for multiple comparisons (Additional file 5: Table S4 and Additional file 6: Figure S1); the great majority of loci, though not all, were relatively hypermethylated in cluster 3 to varying degrees, with such genes as ASCL2, GFI1, IPF1 (or PDX1), IRAK3, ISL1, JAK3, KIT, MME, PENK, RARA, RASSF1, SEPT9, VIM, and WT1 showing the largest differential methylation. This evidence concerns the gene ISL1 and breast neoplasm.