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In agreement with the results presented above, KEGG enrichment analysis indicated that proteins involved in citrate cycle, 2-oxocarboxylic acid metabolism, pyruvate metabolism, carbon metabolism and metabolic pathways were highly enriched (Fig. 7b; Additional file 6: Table S5).
Xenobiotic metabolism signaling and metabolism of xenobiotics by cytochrome P450 pathways were highly enriched in 2,6DNT, 4ADNT, 4ADNT and TNT exposure gene expression profiles.
Several canonical pathways were highly significantly over-represented in activated T cells (Table S7) and included aminoacyl tRNA biosynthesis, purine metabolism, and integrin signaling, which were also identified by the whole exon array data analysis shown in Tables 4 and 5.
IPK analysis suggested that metabolic pathways were highly associated with protein expression in SKBR3 cells while cell motility pathways were highly associated with BT474 cells.
Notably, metabolic pathways were highly perturbed, especially in the 8-week-old mdx muscle.
In the KEGG Orthology enrichment of differentially expressed genes, lipid metabolism pathways were highly represented categories.
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In addition, many pathways were highly-ranked in only a strict subset of the cell lines.
Mitogen-activated protein kinase (MAPK) pathways are highly conserved among yeast, animals, and plants [179].
Clinical pathways are highly useful tools for the systematization and improvement of clinical processes.
ERAD pathways are highly specialized mechanisms that incorporate the basic UPS at their core.
Overall, finding 3 significant and hypothesis-related pathways is highly unlikely (p = 0.0002; binomial test).
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