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To interpret the biological importance of this bicluster, the PANTHER database was used to define significantly enriched functional categories among the 306 probe sets.
The Gene Set Analysis (GSA) package in R was used to define significantly enriched gene categories, here the "Maxmean" statistics was used to calculate enrichment scores, and permutation based p-values were derived from 1000 bootstrap replicates.
To define significantly differential expression genes/exomes, we used a p-value < 0.05 as the cutoff.
A cutoff value of P < 0.05 was used to define significantly enriched pathways.
Significant pathway analysis with entity list FC 1.5 was used to define significantly altered pathways.
We adopted an area by which to define significantly interacting gene pairs based on the data in Figure 2C.
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a,b,c Superscripted letters define significantly different groups, ie results with different letters are significantly different.
13 In the present study, we used a nontargeted metabolomics approach in which we measured 489 metabolites (of both known and unknown annotation) in 206 and 227 participants treated with HCTZ and ATEN, respectively, to define metabolites significantly altered after exposure to either drug and significantly associated with change in HDBP.
Ellis and Perou used the same data to define 28 significantly mutated genes important in therapeutic consideration in breast cancer [ 24].
The common genome-wide level significance threshold (p < 5 × 10-8) was used to define 1,909 significantly trait-associated SNPs from 586 studies.
On the contrary, the result using our approach has 5 sub-networks with defined significantly enriched functions (the largest sub-network has the role of nitrogen fixation, similar to the p = 0.05 case).
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