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A component was determined to be significantly enriched with a particular functional unit if the enrichment score, FDR-corrected P-value ≤0.05.
In our cisplatin case study, by sorting the grid by enrichment score, 177 pathways were found to be significantly enriched with p-value ≤ 0.05 (one-sided Fisher's Exact test).
Performing Fisher's exact tests as a standard enrichment analysis revealed the lysine biosynthesis pathway to be significantly enriched with differentially expressed genes.
However, with improved sequence database annotation, LMs can sometimes be significantly enriched with certain keywords.
However, they are not found to be significantly enriched with any biological process term.
The down-regulated genes were found to be significantly enriched with energy reserve metabolic process (p-value < 0.001).
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For the genes with higher expression in line A, one enriched GO term, heart development, was significantly enriched with fold enrichment of 11.7 (Figure 3A).
The glomerular-enriched genes could be mapped to 105 pathways, 12 of which were significantly enriched with glomerular-associated genes (p<0.05, Fold enrichment >1.5) (Supplementary Table S6).
Interestingly, no functional category was significantly enriched with the closest group being oxidoreductases (enrichment factor of 2.34) (p = 0.069).
Functional enrichment and pathway analysis show that Group I genes are significantly enriched with cell cycle functions whereas Group II genes are biased toward metabolic functions.
Subjected to GO term enrichment analysis, 76% of the corresponding target gene sets were significantly enriched with specific biological process annotations (P < 0.05, Bonferroni corrected).
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