Table 1.
Overrepresented Regulatory, Metabolic, and Hormonal Categories of Each Cluster
| Levels | Count | P Value | Levels | Count | P Value |
| Cluster 1 | Cluster 3 | ||||
| 1. Hormone metabolism | 47 | 1E-04 | 1. Amino acid metabolism | 65 | 1E-05 |
| 1.2 Abscisic acid | 9 | 1E-03 | 1.2 Synthesis | 53 | 6E-07 |
| 1.2 Ethylene | 23 | 2E-06 | 1.2.3 Asp family | 18 | 2E-05 |
| 1.2.3 Signal transduction | 17 | 4E-08 | 1.2.3.4 Misc. homoserine | 5 | 8E-03 |
| 2. RNA | NE | 1.2.3 Branched-chain group | 9 | 1E-03 | |
| 2.2 Transcription regulation | NE | 1.2 Degradation | NE | ||
| 2.2.3 APETALA2/Ethylene-responsive element | 32 | 3E-05 | 1.2.3 Ser-Gly-Cys group | 6 | 2E-03 |
| 2.2.3 WRKY domain | 26 | 1E-07 | 1.2.3.4 Gly | 4 | 3E-02 |
| 3. Stress | NE | 2. Photosynthesis | 47 | 1E-22 | |
| 3.2 Abiotic | NE | 2.2 Light reaction | 27 | 3E-14 | |
| 3.2.3 Heat | 5 | 2E-03 | 2.2.3 Photosystem II | 14 | 9E-10 |
| Cluster 2 | 2.2.3.4 Polypeptide subunits | 14 | 9E-10 | ||
| 1. Glycolysis | 18 | 2E-06 | 2.2.3 Photosystem I | 13 | 4E-09 |
| 1.2 Enolase | 3 | 1E-03 | 2.2.3.4 Polypeptide subunits | 13 | 4E-09 |
| 2. Oxidative pentose phosphate | 10 | 1E-04 | 2.2 Photorespiration | 6 | 6E-03 |
| 2.2 Oxidative pentose phosphate | 6 | 4E-03 | 2.2.3 Gly cleavage | 3 | 1E-02 |
| 3. TCA | 19 | 4E-08 | 2.2 Calvin cycle | 14 | 6E-08 |
| 3.2 TCA | 17 | 4E-09 | 2.2.3 GAP | 4 | 3E-03 |
| 3.2.3 Pyruvate DH | 5 | 5E-03 | 3. Tetrapyrrole synthesis | 22 | 7E-08 |
| 3.2.3 Succinyl-CoA ligase | 3 | 1E-03 | 3.2 Mg chelatase | 4 | 3E-03 |
| 3.2.3 Succinate dehydrogenase | 3 | 1E-03 | 4. Major CHO metabolism | 23 | 2E-02 |
| 4. Mitochondrial electron transport/ATP synthesis | 27 | 1E-16 | 4.2 Synthesis | 23 | 3E-03 |
| 4.2 NADH-DH | 15 | 1E-11 | 4.2.3 Starch synthesis | 1E-03 | |
| 4.2.3 Complex I | 4 | 2E-04 | 4.2.3 Starch degradation | 9E-03 | |
| 4.2.3 Cytochrome C reductase | 6 | 5E-05 | 5. Secondary metabolism | NE | |
| 4.2.3 Cytochrome C oxidase | 6 | 1E-04 | 5.2 Isoprenoids | 26 | 6E-04 |
| 5. Amino acid metabolism | 63 | 8E-19 | 5.2.3 Nonmevalonate pathway | 11 | 3E-03 |
| 5.2 Synthesis | 55 | 3E-21 | 5.2.3 Carotenoids | 6 | 2E-03 |
| 5.2.3 Glu family | 5 | 1E-04 | 6. Lipid metabolism | 46 | 4E-03 |
| 5.2.3.4 Arg | 6 | 2E-05 | 6.2 FA synthesis/elongation | 16 | 1E-03 |
| 5.2.3 Asp family | 15 | 3E-07 | 6.2.3 Pyruvate DH | 4 | 1E-02 |
| 5.2.3.4 Met | 7 | 1E-04 | 6.2 FA desaturation | 5 | 6E-04 |
| 5.2.3.4 Lys | 4 | 4E-03 | 7. Hormone metabolism | NE | |
| 5.2.3 Ser-Gly-Cys group | 9 | 9E-05 | 7.2 Brassinosteroid | 11 | 2E-02 |
| 5.2.3.4 Ser | 5 | 1E-04 | 7.2.3 Synthesis/degradation | 9 | 2E-02 |
| 5.2.3 Aromatic amino acid | 13 | 4E-05 | 7.2.3.4 Sterols | 8 | 6E-04 |
| 5.2.3.4 Chorismate | 6 | 6E-04 | 8. Nucleotide metabolism | NE | |
| 5.2.3.4 Trp | 5 | 5E-03 | 8.2 Salvage | 7 | 1E-02 |
| 6. Nucleotide metabolism | 32 | 1E-10 | 8.2 Deoxynucleotide | 5 | 6E-04 |
| 6.2 Synthesis | 17 | 4E-10 | 9. C1 metabolism | 12 | 6E-04 |
| 6.2.3 Pyrimidine | 6 | 3E-04 | 10. RNA | NE | |
| 6.2.3 Purine | 9 | 3E-06 | 10.2 Transcription regulation | NE | |
| 7. Protein | 24 | 1E-06 | 10.2.3 TCP | 7 | 2E-02 |
| 7.2 Amino acid activation (tRNA ligase) | 16 | 5E-09 | |||
| 7.2 Targeting | 4 | 2E-04 | |||
| 7.2.3 Mitochondria | 3 | 1E-03 | |||
| 8. Cell wall | NE | ||||
| 8.2 Precursor synthesis | 13 | 4E-05 | |||
| 8.2.3 UGD | 3 | 5E-03 | |||
| 9. C1 metabolism | 7 | 7E-03 |
Functional categories that are overrepresented in the list of genes were clustered. Overrepresentation analysis was performed by the PageMan enrichment tool (http://mapman.mpimp-golm.mpg.de/pageman/). Only functional categories with more than three genes are shown. The background genes are available in Supplemental Table 1, and the genes from each cluster are available in Supplemental Table 2. The elaborated analysis is available in Supplemental Table 3. NE, not enriched.