Fig. 2
Specificity and Performance of the SPTBN1 Marker for Melanoma Classification. A Box-and-whisker plot using Tukey’s method, comparing cg04652957 (SPTBN1) methylation levels between 10 SKCM samples and a combined set of 10 samples from each TCGA cancer type plus ten blood samples. The middle line in each box represents the median methylation level. A parametric t-test was used to assess the differences between the groups due to the normal distribution of the data. The significance level (p < 0.0001) is shown on the plot. B ROC analysis of 10 SKCM samples and a combined set of 10 samples from each TCGA cancer type, plus ten blood samples. Sensitivity and specificity values were selected based on the highest likelihood ratio. The AUC value is shown in the figure. C DNA methylation profile of cg04652957 (SPTBN1) across 473 SKCM samples from TCGA, 5006 healthy blood samples, and 8536 tumor samples representing 32 other TCGA cancer types. D DNA methylation profile of cg04652957 (SPTBN1) in normal melanocytes and 31 other healthy tissues. The dataset includes eight healthy melanocyte samples from the GSE122909 cohort and 5323 samples from the EWAS Atlas. The number of samples for each tissue type is as follows (number of samples in parentheses): whole blood (300), brain (300), adipose tissue (300), colon (238), skeletal muscle (211), fallopian tube (182), pancreas (75), stomach (145), prostate (153), thyroid (152), esophagus (125), placenta (300), visceral adipose tissue (142), skin (117), the nasal epithelium (99), testis (87), bone marrow (65), cartilage (59), bone (53), adrenal gland (26), tongue (25), cord blood (286), bladder (26), nasopharynx (25), spleen (15), saliva (300), liver (300), breast (261), lung (298), kidney (299), sperm (300), and normal melanocytes (8). E Comparison of methylation levels across 8 normal melanocyte samples (GSE122909), 195 melanoma samples (GSE144487), and healthy skin samples from GSE51954, GSE90124, GSE115797, and GSE142439. Ordinary ANOVA was used to compare the groups, followed by Tukey’s multiple comparison test to assess differences between each pair of groups. P-values between group pairs are shown on the plot.
