The hash values of a module are compared first, and then role matching is performed again.
The combined TDT p-value for that module was then compared to a distribution of TDT p-values generated from 10,000 randomly sampled modules of the same size, i.e. the final p-value of a module was calculated as by dividing the number of random modules with a better combined p-value with 10,000.
The statistical significance (P-value) of a module's enrichment in a functional set was calculated using Fisher's exact test.
The module eigengene, the first principal component of the matrix of expression values of a given module, was adopted to characterize the gene expression profile of the module [23].
Modules in CAs that show significant overlap (FET_P ≤ 3.1E-06, i.e., Bonferroni corrected p value of 0.05) with a module in AAs and are enriched for SI-associated genes in both ethnicities were considered conserved, while modules enriched for genes associated with SI in only one ethnic group were considered ethnic-specific.
As a conceptual framework for this cost benefit analysis, we suggest that the conservation value of a multiple-use module is a function of the quantity and quality of wildlife habitat in the matrix, the number of species that live in or move through the matrix and the conservation status of these species.
We also suggest that the production value of a multiple-use module – and thus the potential for conservation conflict – is a function of the yield gap of the cropland (potential for intensification) and the quantity and quality of non-cropland in the agricultural matrix that could potentially be cleared to make space for new cropland (potential for expansion).
To assess co-expression perseveration between the species on a module-by-module basis, we first calculated a value of the module membership (MM) - a measure of how well each gene correlates with the first principal component of gene expression within a module, termed as the module eigengene.
ProportionalHill method: a local maxima-based module determination approach, in which the module membership value of a link is determined by the module membership values only of its neighboring links having non lower centrality values (see main text and Section V.2.b. in the Electronic Supplementary Material S1).
GradientHill method: a local maxima-based module determination approach, in which the module membership value of a link is determined by the module membership value(s) only of its neighboring link(s) having maximal centrality values (see Section V.2.b. in the Electronic Supplementary Material S1).
Starting in the 2003/04 academic year, learners were required to rate the instructive value of the module on a Likert scale (1 = not instructive; 5 = highly instructive).
