Table 3.

Single- and multi-omics integration results for gpa2Δ. First block shows GSEA for transcriptomics with adjusted p-value < 0.05, arranged in ascending order; second block shows MetaboAnalystR pathway enrichment analysis for metabolomics with combined p-value < 0.05, arranged in ascending order; third block shows MetaboAnalystR joint pathway analysis with adjusted p-value < 0.05, arranged in ascending order, as detailed in Methods.

Transcriptomics		Metabolomics		Integration
Enriched Pathways	Adjusted p-Value	Enriched Pathways	Combined p-Value	Enriched Pathways	Adjusted p-Value
Ribosome biogenesis in eukaryotes	0.0084	Purine metabolism	0.0021	Oxidative phosphorylation	3.13 × 10−14
Oxidative phosphorylation	0.0084	Fructose and mannose metabolism	0.0047	Galactose metabolism	1.60 × 10−11
		Amino sugar and nucleotide sugar metabolism	0.0079	ABC transporters	1.31 × 10−8
		Galactose metabolism	0.0079	Glycolysis or Gluconeogenesis	8.02 × 10−5
		Glutathione metabolism	0.0155	Fructose and mannose metabolism	8.18 × 10−5
		Tyrosine metabolism	0.0224	Starch and sucrose metabolism	8.18 × 10−5
		Arginine biosynthesis	0.0234	Arginine biosynthesis	0.0012
		Biotin metabolism	0.0252	Pentose phosphate pathway	0.0012
		Aminoacyl-tRNA biosynthesis	0.0360	Purine metabolism	0.0017
		Starch and sucrose metabolism	0.0396	Amino sugar and nucleotide sugar metabolism	0.0073
		Phosphatidylinositol signaling system	0.0424	beta-Alanine metabolism	0.0119
				Alanine, aspartate and glutamate metabolism	0.0139
				Cysteine and methionine metabolism	0.0149
				Citrate cycle (TCA cycle)	0.0221