Table 2.
Analysis of variance of variance
| Source of variation | ave.kME.green, total proportion of variance explained = 15.8% | logPvalue Stouffer, total proportion of variance explained = 6.7% | ||||||
|---|---|---|---|---|---|---|---|---|
| Source | Degrees of freedom | Sums of Sq | Proportion of total variance | F statistic | P-value (F-test) | Sums of Sq | Proportion of total variance | P-value (F-test) |
| PCG (Suz12+Eed+H3K27me3) OccupancyCount | 1 | 49.35 | 0.071 | 2013.0 | < 2.2E-16 | 82,530 | 0.050 | < 2.2E-16 |
| CPG_Island | 2 | 50.78 | 0.073 | 1035.7 | < 2.2E-16 | 24,867 | 0.015 | < 2.2E-16 |
| X chromosome | 1 | 9.74 | 0.014 | 397.4 | < 2.2E-16 | 764 | 0.000 | 5.5E-04 |
| Distance to TSS | 1 | 3.50E-01 | 0.001 | 14.1 | 1.7E-04 | 1,827 | 0.001 | 9.3E-08 |
| Residual error | 23,903 | 586.02 | 0.842 | 1,529,855 | 0.933 | |||
| Total variation | 696.24 | 1,639,843 | ||||||
The first six columns detail the sources of variation on ave.kME with respect to the green (aging) module. Polycomb group occupancy count explains the highest proportion of the total variance followed by CpG island status (inside, outside, and shore). Comparing the results from ANOVA applied to average kME with those from applying it to the logP-value (significance measure resulting from Stouffer's meta-analysis) reveals marked differences in the proportion of variance explained (15.8% versus 6.7%), which suggests again that the average kME measure is biologically more meaningful than the meta-analysis P-value. TSS, transcription start site.