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10 The most impacted pathways were obtained by evaluating those pathways with calculated impact values above 50% of the total impact value of the top-impacted pathway independently at 60 vs. 0 (early growing phase), 120 vs. 60 (late growing phase), and 220 vs. 120 (finishing phase).
The regulation of the cytoskeleton was one of the most impacted pathways.
In addition, 5 pathways of the Immune System Diseases sub-category were among the 25 most impacted pathways in the DIA analysis (Additional File 2: Sheet 'DIA KEGG'DIA
Galactose metabolism, one carbon pool by folate, glyoxalate and dicarboxylate metabolism, and linoleic acid metabolism were among the 25 overall most impacted pathways among the metabolism subcategories.
By using genomic and bioinformatics approaches to analyse the generated mRNA profiles, we uncovered that the most impacted pathways by the EGCG treatment are the networks related to AKT, NF-κB, MAP kinases, and cell cycle regulation.
Cell cycle regulation and inflammation were found to be the most impacted pathways by EGCG [ 21], suggesting that the anti-cancer activity of green tea polyphenols is mediated by inhibiting cell proliferation and anti-inflammation.
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The overall most-impacted pathway was fatty acid biosynthesis.
The former was used to determine the most impacted canonical pathways, while DAVID was used to determine the most relevant subcategories within the 3 gene ontology domains (cellular component, molecular function, and biological processes).
When only the finishing phase was considered (220 vs. 120), GPI-anchor biosynthesis (Glycan Biosynthesis and Metabolism subcategory), Pentose and glucuronate interconversions (Carbohydrate Metabolism subcategory), and Sulfur metabolism (Energy Metabolism subcategory), in that order, were the most impacted metabolic pathways.
This latter study, though examining soybean root knot nematode interplay, reveals cell wall modeling, defense response, and metabolism, to be the most impacted host pathways following pathogenic nematode infection.
Among the relevant GO biological process (GOT-ERM_BP_FAT) that were among the top 20 most impacted and activated pathways in this category were positive regulation of activin receptor signaling pathway, muscarinic acetylcholine receptor signaling pathway, long-chain fatty acid transport, and negative regulation of myoblast differentiation (Fig. 6; Suppl 2: Adipose DIA sheet).
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