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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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Unlike PE, this work ensures parameter convergence by imposing a newly defined, significantly milder, and online verifiable initial excitation (IE) assumption.
As for OS, the ERCC1-118 and the XPD 751 SNPs defined significantly different survival groups of patients.
We further defined significantly expressed probes as those with a P-value < 0.05 and ≥1.2-fold change from baseline.
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).
Of the other 10, we compute the 3 most densely connected hubs for each sub-network, and in 2 of 10 such sub-networks, the hubs have defined significantly enriched functionalities.
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