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.

Horvath et al. Genome Biology 2012 13:R97   doi:10.1186/gb-2012-13-10-r97

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