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The results show that many of these clusters represent expected downstream effects of the TOR pathway, including changes in nitrogen metabolism, actin polymerization, and autophagy, as well as a large module of RNA processing genes.
A widespread effect of aging was increased expression of inflammation and immune response genes, which involved class I MHC genes (e.g., H2-D1, H2-K1), immunoglobulin chain components (e.g., Igk-V1, Igh-6), and a large module of 40 co-expressed genes known to participate in inflammation and immune processes (see Figures 5 and 6; Additional File 10).
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The different functions of the smaller parts of a large module can play pivotal roles in transplantation.
In general, large modules own high recall value because a large module C contains a lot of nodes in the set of F, and extremely, all nodes are gathered in the same cluster; in this case the recall value tends to the highest.
This is important because some cellular functions may involve a single direct protein interaction (small scale), whereas others require more and/or indirect interactions, such as protein complexes (medium scale) and interactions between large modules of proteins (large scale).
The module containing DNA packaging and structural proteins is the largest module of the Sf101 phage, and is predicted to contain 15 orfs (orf 1 to 15).
If a large enough module of genes within the pathway is co-expressed, then one factor will capture the same pattern of co-expression across individuals.
The two largest modules of the coexpression network, module A (2848 genes) and module B (2861 genes), grouped genes with strong general responses to the pathogen.
In SSIM, a larger preference value of affinity propagation [ 27] means that every gene is more likely to be an exemplar of a module (module center), which would produce a large number of modules composed of highly similar genes in terms of integrated similarity and allow us to view the system in detail.
In the intrinsic network for lung cancer (NSCLC), a small set of gatekeeper modules cooperate with a large number of modules (in terms of outcome prediction).
The basic structural motif of the HECT E3 ligases is a large C-terminal module of circa 350 residues.
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