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].
Therefore, a synthetic design principle can either be to construct modules that are robust to noise or to explicitly use the stochastic nature of the cellular environment in the design process.
It involves many well-documented genes that can be used as references to validate the bioinformatic analyses as well as to construct modules of co-expressed and interacting genes.
Each newly constructed module is checked in terms of overlap with the rest of the modules that have been previously created.
Genetic engineering to modify cells involves constructing modules of functional gene sequences.
The simplification may be carried on by constructing modules of modules.
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).
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].
