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The results of the analysis showed that the networks of the differentially expressed genes reflected the embryonic origin of the genes (Figure 3).
To evaluate whether the differentially expressed genes reflected specific biological functions, we assigned them to gene ontology (GO) categories.
Functional categorization of differentially expressed genes reflected a number of important pathways, including the de novo FA biosynthesis, TAG assembly and the formation of PUFAs.
Another limitation was the difficulty distinguishing whether differentially expressed genes reflected OA progression in cartilage, differences in innate bone structure, or were driven by changes in mechanical loading.
Altogether, hPGCLCs, TCam-2, and hPGCs share key germ cell characteristics and expressed the core germ cell genes, including CD38, whereas the differentially expressed genes reflected their corresponding stages of development and cell identity.
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Interestingly, theorgan-enriched, differentially expressed genes reflect known organ-specific biological activities.
Our results confirm the authors' initial observations [ 8] that many of the differentially expressed genes reflect changes in infiltration by inflammatory cells and connective tissue.
"Metabolism (01)" and "Transport facilitation (67)" were represented as two major functional classes with differentially expressed genes, reflecting need for uptake and metabolism of two different carbon sources.
If the modifier theory is correct, then one might expect a greater overlap between the sets of differentially expressed genes reflecting a shared mechanism.
These results suggest that differentially connected genes reflect the dynamic process of changes in the biological system, whereas differentially expressed genes reflect the end result of biological system changes.
Moreover, hierarchical clustering using expression data from purified monocytes provided significantly improved discrimination between the patient groups than that obtained using PBMC data, presumably because the differentially expressed genes reflect genuine differences in processes underlying disease pathogenesis.
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