We then plotted the number of genes with and without a single reproducible associated peak classified separated into several bins of expression.
Descriptive statistics for peaks classified into the six groups are summarized in Table 2.
Several peaks, classified as "overlap" , (partially) cover two or more ORFs (Additional file 5: Figure S3).
Three types of signals were present at the CpG-sites: 1) A T-peak and no C-peak; classified as an unmethylated CpG-dinucleotide 2) A C-peak and no T-peak; classified as a methylated CpG-dinucleotide 3) Superimposing C- and T-peaks; classified as heterogeneously methylated CpG-dinucleotide.
High intensities of all peaks occurring in fifth and sixth peak cluster groups, including the hsp27 peak, classify patients into subcohorts I and III corresponding to luminal A subtype of tumors with high expression of ER.
Figure 4B shows the expression profiles of the top two ranked marker peaks for classifying the characteristic of lymph node involvement.
The area under the ROC (Receiver Operating Characteristic) curve (AUC) was estimated per peak to evaluate the performance of a peak to classify samples into the two groups.
No single peak successfully classified with an accuracy of greater than 95%.
All remaining 2 kbp sites centered on an Pol2 peak were classified as promoter-distal.
Tumors with a single G0/G1 peak were classified as DNA diploid (DNA-index of 1.0).
