Focusing on TFs undergoing both CNV loss and promoter hypermethylation (at least 1 % frequency for both types of alteration) revealed only a few (EBF1 in LSCC, LYL1 in LUAD, ZNF287 in BLCA and HIC1 in COAD) which did so in a mutually exclusive fashion, in the sense of exhibiting higher levels of hypermethylation in tumours with no CNV loss of the given TF, compared with tumours with CNV loss, although this was only evident if the previous threshold for calling significant promoter hypermethylation (i.e. 0.3) was relaxed to a value of 0.1 (Additional file 1: Figure S16). This evidence concerns the gene EBF1 and bladder transitional cell carcinoma.