Table 1. Summary of changes in methylation level/variance categories between normal and cancer datasets.
We assigned each gene to a category that indicated whether it was methylated at low, medium, or high levels and whether it had low or high variance across samples in a given dataset. The table shows the total number of genes in each category for the normal datasets and the number (and percentage) of genes that changed from one category to another in the tumor datasets.
| Normal category | Tumor category | Total # genes (normal) | # genes changed | % genes changed |
|---|---|---|---|---|
| Low methylation/low variance | High methylation/low variance | 12,826 | 86 | 0.67 |
| Low methylation/low variance | Low methylation/high variance | 12,826 | 1,568 | 12.2 |
| Low methylation/low variance | Medium methylation/high variance | 12,826 | 88 | 0.69 |
| Low methylation/low variance | Medium methylation/low variance | 12,826 | 382 | 2.98 |
| Low methylation/high variance | High methylation/low variance | 118 | 4 | 3.39 |
| Low methylation/high variance | Low methylation/low variance | 118 | 43 | 36.4 |
| Low methylation/high variance | Medium methylation/high variance | 118 | 4 | 3.39 |
| Low methylation/high variance | Medium methylation/low variance | 118 | 3 | 2.54 |
| Medium methylation/low variance | High methylation/high variance | 3,274 | 1 | 0.03 |
| Medium methylation/low variance | High methylation/low variance | 3,274 | 743 | 22.7 |
| Medium methylation/low variance | Low methylation/high variance | 3,274 | 277 | 8.5 |
| Medium methylation/low variance | Low methylation/low variance | 3,274 | 244 | 7.5 |
| Medium methylation/low variance | Medium methylation/high variance | 3,274 | 150 | 4.6 |
| Medium methylation/high variance | High methylation/low variance | 10 | 4 | 40.0 |
| Medium methylation/high variance | Low methylation/high variance | 10 | 1 | 10.0 |
| Medium methylation/high variance | Medium methylation/low variance | 10 | 2 | 20.0 |
| High methylation/low variance | High methylation/high variance | 3,576 | 1 | 0.03 |
| High methylation/low variance | Low methylation/high variance | 3,576 | 27 | 0.76 |
| High methylation/low variance | Low methylation/low variance | 3,576 | 4 | 0.11 |
| High methylation/low variance | Medium methylation/high variance | 3,576 | 136 | 3.8 |
| High methylation/low variance | Medium methylation/low variance | 3,576 | 583 | 16.3 |