Fig. 4

The COL17A1 promoter methylation status predicts the direction of misexpression in breast and cervical cancer. a COL17A1 allelic copy number gains and losses in relation to normalized COL17A1 expression level. Data are extracted from TCGA breast cancer RNAseq V2 RSEM and SNP6 array GISTIC copy number datasets. Error bars represent standard error of the mean. p values: Mann-Whitney U test. b Heat map of the degree of promoter methylation based on β values for each indicated probe. Each three-probe column corresponds to a sample. Data were extracted from the TCGA Illumina Infinium HumanMethylation450 breast cancer dataset [21, 22]. c Box plot for COL17A1 promoter methylation comparing normal samples to all samples, as well as to samples with indicated allelic copy numbers. Whiskers represent 10–90 percentiles of the data. p values: Mann-Whitney U test. d Scatter plot of COL17A1 promoter methylation compared to normalized COL17A1 gene expression. p value for linear regression line: Spearman correlation. e–h Graphs as in (a–d), respectively, for cervical cancer. Data were derived from the TCGA cervical dataset. p value summaries: n/s not significant; *p < 0.05; **p < 0.01; ****p < 0.0001