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It appears that the gradual, stochastic course of gene death is punctuated by occasional bursts when a gene belonging to a functional module or pathway is eliminated, rendering useless the remaining genes in the same module or pathway.
This score is used to determine the relative importance of the corresponding module or pathway in different patient groups.
The concept of robustness refers to the 'purpose' of a certain module or pathway: it is expected that intracellular network structures have undergone an evolution that guarantees their proper functioning independently of precise parameter values [ 56].
This suggests that aberrant DNA methylation in cancer is characterized by a modularity in the sense that many components of the same gene module or pathway may be affected in the same sample.
At the module or pathway levels, the fecal microbiota of the HBLC patients showed enrichment in the metabolism of glutathione, gluconeogenesis, branched-chain amino acid, nitrogen, and lipid (P < 0.05), whereas there was a decrease in the level of aromatic amino acid, bile acid and cell cycle related metabolism (P < 0.05).
There are so far only few examples for WGD-derived functional module or pathway duplications: the starch biosynthesis pathway in rice (Wu et al. 2008), the C4 photosynthetic pathway in grasses (Wang et al. 2009), the egesterol pathway in the fungus Rhizopus oryzae (Ma et al. 2009), and presumably the core network of cartilage development in vertebrates (Hecht et al. 2008).
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It represents the chance that at least k CPP metabolites co-exist in the same module, cluster or pathway.
In order to identify features that are associated with a clinical phenotype of interest, features can be mapped onto a priori defined and manually curated modules or "pathways".
Overlapping component genes serve as bridges across these relatively independent functional modules or pathways, hence perturbation in one pathway such as the BMP-TGF-beta signaling pathway can be propagated throughout other relevant pathways.
Such analyses, when applied in the metabolic context, can be thought of as pathway finding methods, uncovering linked modules (or pathways) of genes or proteins that undergo coordinated change as a result of some environmental or genetic perturbation.
Besides technical factors, the disparity may result from the fact that diseases are directly caused by the perturbations of the molecular function that are generally carried out by a set of genes in the form of modules or pathways.
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