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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