KIT and breast neoplasm: 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.