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Immunity-related pathways were selected for further analysis, and our results demonstrated that a total of 13 and 50 DEGs were annotated in the humoral immune-related and cellular immune-related pathways, respectively.
Process and pathways were selected based on a p-value < 0.05.
These pathways were selected on the basis of corrected gamma p value ≤0.05 and a minimum input of 4 genes.
Key genes forming focus hubs within significantly modulated interaction networks from, GO groups and canonical pathways were selected for in vivo validation.
In this study, pathways were selected as significant based on a consensus of the results obtained with two normalization algorithms, and two probe set sorting criterions.
The EGFR and Rho signaling pathways were selected since EGF is known to be required for nsph propagation and CSPG signals via RhoA in neurons.
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It remains unclear how these pathways are selected and regulated.
When multiple pathways are selected at the same time, the view will show all unique gene components within selected pathways.
Notably, when using elastic net, we select correlated variables in groups ensuring that genes operating in pathways are selected together.
The pathway gene method is a combination of both methods; instead of candidate genes, candidate pathways are selected based on the pharmacodynamic and pharmacokinetic behaviour of a drug.
Given the more compute-intensive nature of the latter, if a subset of pathways is selected, only reactions in those pathways will be included in the variability analysis.
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