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Exact(4)
Of the 40 modules found by AMBIENT, all of the up-regulated modules were significant with a q-value (p-value corrected for multiple testing) of < 0.05 and six down-regulated modules were significant.
Within these, the midnightblue, red and cyan modules were significant for a trait of interest, as mentioned earlier.
A total of ten modules were significant (p ≤ 0.05, size >2), and were manually inspected (Table 2).
For example, ~40% of the tested gene modules were significant at a level of 0.05 when using MMC, while ~25% and 30% were significant when using Pearson and SVA, respectively.
Similar(56)
To assess whether the number of genes in consensus modules is significant, we perform a permutation test.
However, it is worth noting that the basicranial module is significant in only a small majority of primate species, as reflected in the bootstrap analyses of mean within-module correlation across species (Table 1).
For the induced and repressed genes separately, we test whether the overlap of induced or repressed genes on the array with the module is significant, compared to a random draw.
In agreement with this, a cation antiport module was significant upregulated (p ≤ 9.0E-5, 8/17 nodes RanaUp).
This module is significant and the genes CDKN2B and CDK4/TSPAN31 are mutually exclusive with p1 <0.001 and p2 <0.001.
The module eigengene correlation for the Red module was significant in both the A/J (r = 0.99, p = 2.4e-16 2.4e-167BL/6J (r = 0.99, p = 5.4e-14) networks.
This single term was not enriched in the NSGG (FDR = 99.8); however, its enrichment in the turquoise module was significant (FDR = 1.1 × 10−3).
Related(13)
nodes were significant
clusters were significant
models were significant
examples were significant
simulations were significant
modes were significant
elements were significant
dimensions were significant
components were significant
cycles were significant
samples were significant
contents were significant
modules showed significant
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