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The results from our study suggest that the magnitude of the effect of strain and brain region is about the same, as module significance and eigengene values are comparable.
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There are no measures of module significance per se, and the actual module structure may change if different cutoffs are chosen in the analysis (see Supplementary File 2).
In an attempt to find correlations of significant modules with gene expression profiles, we also defined GS i and module significance (MS) network metrics.
The pink module (114 genes) was therefore finally selected on the basis of the strongest positive correlation with a stage and slightly higher module significance in comparison with the black and turquoise modules.
To determine which genes and modules were related to lesion size, we calculated two metrics, the Gene Significance (GS) and Module Significance (MS).
The R package WGCNA implements a suite of tools for network construction, module detection, module significance examination, module preservation computation, and hub gene query, among many others [ 29– 31].
The module significance of the Yellow module genes corresponds to p values 0.006, 0.01 and 3.5 × 10-7 in datasets 1, 2 and 3, respectively.
Module significance for either a continuous or dichotomous outcome is determined assessing eigengene module significance.
We defined two related measures of module significance.
The first measure of module significance is simply the average gene significance measure across module genes.
We defined a measure of module significance as average absolute gene significance across the module genes.
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