Thirdly, a WGCNA approach was used to discover possible modules consisting of groups of genes with similar transcript abundance, either across time or between genotypes of both, and 27 modules out of a total of 47 modules showed significant variation in transcript abundance across time points or genotypes or their combinations (Additional file 8: Table S5; Additional file 9: Figure S4A-C).
Modular PKS and NRPS are enzymes that devote separate modules, consisting of groups of catalytic domains, to each elongation step of the growing molecular chain.
Recently, this reticulate classification was extended to shared evolutionarily conserved modules consisting of groups of proteins that have a similar phylogenetic profile (Lima-Mendez et al., 2011).
Modules consist of groups of biomolecules (genes, proteins, or gene products in general) that are found (often by different statistical approaches) to regulate as a unit a biological property or phenotype.
To show the consistent results at different thresholds, we also illustrated the modules of three groups at sparsities of 7%and9%9%.
The modules of three groups' mean networks nearly decreased as a function of increase in connection density.
At 9% ≤ sparsity ≤ 10%, there were only five modules in our healthy controls which would limit the illustration of modules of three groups.
To verify our findings about the altered modular structures in cirrhotic patients, we also demonstrated the modules of three groups at the 7% and 9% sparsities (Supplementary Figures 2 and 3).
Figure 2 shows the total number of modules of each group's mean network over the entire range of sparsity.
Shown are the absolute correlation coefficients between trait pairs from modules of different grouping methods (left to right: random, GEMOT, HC, and INVAMOD; x -axis).
