Table 4.

Single- and multi-omics integration results for ras2Δ. 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
Starch and sucrose metabolism	0.0065	Lysine biosynthesis	1.00 × 10−5	Galactose metabolism	1.24 × 10−15
Oxidative phosphorylation	0.0065	Glyoxylate and dicarboxylate metabolism	0.0005	Starch and sucrose metabolism	1.68 × 10−11
Ribosome biogenesis in eukaryotes	0.0065	Glycine, serine and threonine metabolism	0.0009	Glycolysis or Gluconeogenesis	6.26 × 10−8
Ribosome	0.0065	Arginine biosynthesis	0.0017	Glycine, serine and threonine metabolism	4.30 × 10−6
RNA polymerase	0.0092	Cysteine and methionine metabolism	0.0028	ABC transporters	1.03 × 10−5
Galactose metabolism	0.0169	Taurine and hypotaurine metabolism	0.0043	Pentose phosphate pathway	2.27 × 10−5
Autophagy	0.0169	Amino sugar and nucleotide sugar metabolism	0.0043	Cysteine and methionine metabolism	2.27 × 10−5
Meiosis	0.0332	Galactose metabolism	0.0043	Fructose and mannose metabolism	0.0002
Spliceosome	0.0458	Butanoate metabolism	0.0095	Amino sugar and nucleotide sugar metabolism	0.0002
		Lysine degradation	0.0098	Arginine biosynthesis	0.0003
		Aminoacyl-tRNA biosynthesis	0.0098	Purine metabolism	0.0005
		Starch and sucrose metabolism	0.0204	Glyoxylate and dicarboxylate metabolism	0.0009
		Alanine, aspartate and glutamate metabolism	0.0372	Peroxisome	0.0014
		Fructose and mannose metabolism	0.0384	Methane metabolism	0.0057
		Nitrogen metabolism	0.0392	Alanine, aspartate and glutamate metabolism	0.0057
		Phosphatidylinositol signaling system	0.0429	Lysine biosynthesis	0.0213
				Nitrogen metabolism	0.0255
				Citrate cycle (TCA cycle)	0.0338
				Vitamin B6 metabolism	0.0385
				Inositol phosphate metabolism	0.0390
				Monobactam biosynthesis	0.0392
				Tryptophan metabolism	0.0464