Table 4 Summary of over-represented KEGG pathway terms in each subset of yeast data
From: Partitioning of functional gene expression data using principal points
Category (Annotated / Total, %) | Term | KEGG id | count | p-value | FDR (E-2: 10−2) |
|---|---|---|---|---|---|
Subset 1 (36/106, 33%) | DNA replication | ko03030 | 10 | 6.10E-09 | 2.40E-07 |
Mismatch repair | ko03430 | 7 | 2.20E-06 | 4.30E-05 | |
Cell cycle - yeast | ko04111 | 11 | 1.80E-04 | 2.30E-03 | |
Amino sugar and nucleotide sugar metabolism | ko00520 | 6 | 4.70E-04 | 4.70E-03 | |
Pyrimidine metabolism | ko00240 | 8 | 6.70E-04 | 5.40E-03 | |
Base excision repair | ko03410 | 4 | 6.00E-03 | 3.90E-02 | |
Nucleotide excision repair | ko03420 | 5 | 7.30E-03 | 4.10E-02 | |
Starch and sucrose metabolism | ko00500 | 5 | 9.60E-03 | 4.70E-02 | |
Galactose metabolism | ko00052 | 4 | 1.40E-02 | 5.90E-02 | |
Purine metabolism | ko00230 | 7 | 1.50E-02 | 5.90E-02 | |
Meiosis - yeast | ko04113 | 7 | 4.90E-02 | 1.70E-01 | |
Homologous recombination | ko03440 | 3 | 6.10E-02 | 1.90E-01 | |
Fructose and mannose metabolism | ko00051 | 3 | 7.30E-02 | 2.10E-01 | |
Subset 2 (14/123, 11%) | MAPK signaling pathway - yeast | ko04011 | 6 | 6.00E-04 | 1.20E-02 |
Cell cycle - yeast | ko04111 | 8 | 1.20E-03 | 1.20E-02 | |
Meiosis - yeast | ko04113 | 7 | 7.10E-03 | 4.90E-02 | |
DNA replication | ko03030 | 3 | 7.00E-02 | 3.20E-01 | |
Subset 3 (195/821, 23%) | Metabolic pathways | map01100 | 136 | 3.90E-09 | 3.80E-07 |
Biosynthesis of secondary metabolites | map01110 | 65 | 1.20E-05 | 5.80E-04 | |
Glycerophospholipid metabolism | ko00564 | 14 | 5.50E-04 | 1.70E-02 | |
Carbon metabolism | ko01200 | 29 | 5.70E-04 | 1.40E-02 | |
Tyrosine metabolism | ko00350 | 7 | 6.10E-03 | 1.10E-01 | |
Glycolysis / Gluconeogenesis | ko00010 | 16 | 6.70E-03 | 1.00E-01 | |
Propanoate metabolism | ko00640 | 6 | 9.30E-03 | 1.20E-01 | |
Fatty acid elongation | ko00062 | 5 | 1.40E-02 | 1.50E-01 | |
Biosynthesis of antibiotics | map01130 | 41 | 1.70E-02 | 1.70E-01 | |
Fatty acid metabolism | ko01212 | 8 | 1.90E-02 | 1.70E-01 | |
Oxidative phosphorylation | ko00190 | 17 | 2.30E-02 | 1.80E-01 | |
Pyruvate metabolism | ko00620 | 11 | 2.70E-02 | 2.00E-01 | |
Starch and sucrose metabolism | ko00500 | 11 | 3.20E-02 | 2.10E-01 | |
Glycosylphosphatidylinositol(GPI)-anchor biosynthesis | ko00563 | 8 | 3.90E-02 | 2.40E-01 | |
Mismatch repair | ko03430 | 7 | 4.00E-02 | 2.30E-01 | |
Phenylalanine metabolism | ko00360 | 5 | 4.70E-02 | 2.50E-01 | |
Biosynthesis of unsaturated fatty acids | ko01040 | 5 | 4.70E-02 | 2.50E-01 | |
Protein processing in endoplasmic reticulum | ko04141 | 18 | 5.50E-02 | 2.70E-01 | |
Arginine biosynthesis | ko00220 | 6 | 6.40E-02 | 3.00E-01 | |
MAPK signaling pathway - yeast | ko04011 | 12 | 6.60E-02 | 2.90E-01 | |
Methane metabolism | ko00680 | 8 | 6.70E-02 | 2.90E-01 | |
Degradation of aromatic compounds | ko01220 | 4 | 7.80E-02 | 3.10E-01 | |
Other types of O-glycan biosynthesis | ko00514 | 5 | 8.20E-02 | 3.10E-01 | |
N-Glycan biosynthesis | ko00510 | 8 | 9.20E-02 | 3.30E-01 | |
Fatty acid degradation | ko00071 | 6 | 9.60E-02 | 3.30E-01 | |
Subset 4 (191/1113, 17%) | Ribosome biogenesis in eukaryotes | ko03008 | 33 | 2.40E-05 | 2.30E-03 |
RNA transport | ko03013 | 34 | 2.40E-05 | 1.20E-03 | |
Purine metabolism | ko00230 | 34 | 5.10E-05 | 1.70E-03 | |
RNA polymerase | ko03020 | 15 | 2.40E-04 | 5.70E-03 | |
Steroid biosynthesis | ko00100 | 9 | 5.20E-03 | 9.50E-02 | |
Biosynthesis of amino acids | ko01230 | 33 | 1.30E-02 | 1.80E-01 | |
Proteasome | ko03050 | 13 | 1.40E-02 | 1.80E-01 | |
Non-homologous end-joining | ko03450 | 6 | 2.00E-02 | 2.20E-01 | |
Pyrimidine metabolism | ko00240 | 21 | 2.20E-02 | 2.20E-01 | |
RNA degradation | ko03018 | 18 | 3.30E-02 | 2.80E-01 | |
Cysteine and methionine metabolism | ko00270 | 12 | 4.30E-02 | 3.20E-01 | |
Phosphatidylinositol signaling system | ko04070 | 7 | 5.00E-02 | 3.40E-01 | |
Biosynthesis of antibiotics | map01130 | 49 | 6.00E-02 | 3.70E-01 | |
Subset 5 (407/1809, 22%) | Metabolic pathways | map01100 | 239 | 2.60E-05 | 2.70E-03 |
Biosynthesis of secondary metabolites | map01110 | 113 | 1.90E-04 | 1.00E-02 | |
Protein processing in endoplasmic reticulum | ko04141 | 40 | 6.50E-04 | 2.20E-02 | |
Biosynthesis of antibiotics | map01130 | 84 | 1.40E-03 | 3.60E-02 | |
Basal transcription factors | ko03022 | 18 | 3.10E-03 | 6.30E-02 | |
mRNA surveillance pathway | ko03015 | 23 | 4.50E-03 | 7.50E-02 | |
Endocytosis | ko04144 | 31 | 9.50E-03 | 1.30E-01 | |
Ubiquitin mediated proteolysis | ko04120 | 22 | 1.40E-02 | 1.70E-01 | |
Spliceosome | ko03040 | 33 | 1.50E-02 | 1.70E-01 | |
Phagosome | ko04145 | 17 | 3.20E-02 | 2.90E-01 | |
Biosynthesis of amino acids | ko01230 | 46 | 3.40E-02 | 2.80E-01 | |
Glycine, serine and threonine metabolism | ko00260 | 15 | 5.00E-02 | 3.60E-01 | |
Citrate cycle (TCA cycle) | ko00020 | 15 | 5.00E-02 | 3.60E-01 | |
Arginine and proline metabolism | ko00330 | 11 | 5.20E-02 | 3.50E-01 | |
Proteasome | ko03050 | 16 | 5.20E-02 | 3.30E-01 | |
Phenylalanine, tyrosine and tryptophan biosynthesis | ko00400 | 9 | 8.50E-02 | 4.60E-01 | |
Glyoxylate and dicarboxylate metabolism | ko00630 | 12 | 9.80E-02 | 4.90E-01 | |
Valine, leucine and isoleucine biosynthesis | ko00290 | 7 | 9.90E-02 | 4.80E-01 |