We constructed modules from all three algorithms using default parameters (the module creation is independent of any expression data).
Among the 548 constructed modules, only 12 modules showed significant association with PrCa status (FDR < 0.05) and were preserved in the testing dataset (Zsummary > 5).
However, the genes in V C might have many interactions with the genes in gene set V and potentially provide important information in representing the biological function of the constructed modules.
Agrobacterium tumefaciens strain containing the 3′ DIII construct module was codelivered into N. benthamiana leaves along with the 5′ module and an integrase construct through agroinfiltration [ 27, 28].
Genetic engineering to modify cells involves constructing modules of functional gene sequences.
The simplification may be carried on by constructing modules of modules.
An alternative to model the large number of genes is to construct modules (clusters), where each module is composed by several genes, and then, to construct the module-module networks [ 18- 20].
This algorithm constructs modules around a seed protein and it is noteworthy that the size of module remained the same even after the DMSP stage.
Therefore, these approaches would not be expected to be maximally effective in constructing modules with strong association to biological functions [ 16, 17].
Using our R software tutorial, the reader can easily verify that our conclusions are highly robust with respect to a) different ways of constructing co-expression networks and b) different ways of constructing modules.
