Furthermore, the blue, black, brown, and turquoise modules possess a significant amount of lncRNAs (Supplementary Table S3) and thus are interesting modules to examine the relationships between lncRNAs and known ID genes.
Because reactions in each module possess positively correlated functional features, or flux variation pattern, we speculate that BN with representative reactions would reveal a reasonable system-wide causal network that shows correlations among their corresponding metabolic modules as well in response to specific perturbations.
In this strain, the final extension module of MlsB possesses an AT domain with propionate rather than acetate specificity, suggesting natural recombination within mlsB [ 18].
In summary, our analysis reveals that the GO-term specific collection of DECOB modules possesses the better predictive power, since it reveals well-known, relevant and predicts plausible, interesting relationships that other methods miss.
To measure the accuracy of module predictions we used a leave-one-out (LOO) cross-validation procedure, i.e. only proteins which itself and one of its module components possessed an annotation were used in cross-validation.
The structure function relationships of BthChi74 are discussed in relation to other chitinases, such as Listeria chitinase, which possesses a family 5 carbohydrate-binding module (CBM5).
The VKR receptor possesses a Venus Fly Trap (VFT) extracellular module, a bilobate structure that binds small ligands to induce receptor kinase activity.
Moreover, an SH3BP1 splice-variant BARGIN (BGIN), which possesses a C-terminus polyubiquitin (Ub) binding module, inactivates Rac1 in a poly-Ub-interaction dependent manner.
In soluble plasma FN, only one subunit possesses a V domain, and the EIIIB and EIIIA modules are absent [ 14- 16].
