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Of the 9,982 significant probes, 3300 had a Δbeta of more than 0.1, meaning that the mean methylation values between groups are different by more than 10%, which we refer to as differentially methylated probes (DMPs, Figure 2a, Additional file 2: Table S2).
CpGs methylated or unmethylated in cases and controls, as well as CpGs with mean methylation values between 0.25 and 0.75 (partially methylated) in the control samples, were not considered for further analyses.
The centroids of the methylation subgroups were defined as the mean methylation values of the 9,886 melanoma-methylated and 5,236 melanoma-demethylated CpGs, across each subgroup of the Bergen samples.
identified three distinct groups for which mean methylation values significantly differed.
All mean methylation values were log-transformed after adding an offset value of 1.
Mean methylation values for LDLR were as follows: control, 0.42; LB, 0.38; NoB, 0.39 (ANOVA, P value < 0.0001).
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Cohort 2 was divided into four age classes 20-455, 461-75 61-75, 76-97) and for each amplicon, mean methylation value and mean standard deviation were calculated.
The software gives a mean methylation value for each 10 CpG site and the total mean of all 10 CpG sites.
In support of this classification, the mean methylation value (β-value) in subtype H tumors was twice that observed in subtype L (0.603 vs. 0.305, respectively; P < 0.001).
Amplification must have been present in at least two of the three reaction wells in the triplicate run, and the β-actin-normalised mean methylation value must have fallen within the range of the serial standard curve dilutions.
Transcription factors are highlighted with a † Since the predictive power of multivariate models based on all CpG probes in a CGI + SS is larger than the predictive power of the mean methylation value only, we now investigate which CpG in a CGI + SS are particularly important predictors of expression.
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