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Most functional classes are consistent with stromal as opposed to tumour cell function (e.g., proteinaceous extracellular matrix P=2.37 × 10−08, extracellular matrix P=2.49 × 10−08, collagen triple helix repeat P=7.12 × 10−07), although genes known to be expressed in tumour epithelium were identified (e.g., GREM1).
Yook et al. [6] have concluded that most functional classes appear as segregated sub-networks of the full protein interaction network (PIN).
The number of genes in most functional classes has increased since that original annotation [ 5].
Remarkably, most functional classes of proteins with a significant conservation signal were highly specific for the signal within one group of domains, but not in other groups.
This analysis revealed that the distribution of DEGs in most functional classes varied depending on the fruit developmental stage (Fig. 5).
However, at 20 120 min after CORM-3 addition, genes in most functional classes are down-, not up-, regulated in both strains (Fig. 3A).
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Two of the most prevalent functional classes that show clear function-expression coherence are genes involved in sexual reproduction and host immune response.
Among the probe sets which were down-regulated in the resistant genotype over the susceptible genotype, the most abundant functional classes were metabolism (35.1%), proteins with binding function (24.1%), and systemic interaction with the environment (10.9%).
For down-regulated probe sets the most abundant functional classes in the incompatible interaction (Fig. 4b) were proteins with binding function (34.7%), metabolism (29.6%), and genes involved in protein fate (20.3%), whereas in the compatible interaction the most abundant classes (Fig. 4b) were proteins with binding function (36%), metabolism (30.4%), and genes involved in transcription (14.4%).
Non-synonymous variants were found in most functional gene classes including genes involved in general metabolism, cytoskeletal structure, and extracellular matrix formation (Additional file 8: Table S10).
Taken together, the data support a model in which the X has a slightly lower mutation rate but nevertheless experiences a higher substitution rate at most functional sequence classes owing to a greater efficacy of positive natural selection (Charlesworth et al. 1987; Kirkpatrick and Hall 2004).
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