Table 7. Enriched gene ontology (GO) terms associated with selected expression categories of shoot differentially expressed genes.
| Group1 | Enriched GO term | Analysis method2 | ||||
|---|---|---|---|---|---|---|
| i.d. | Category3 | Position4 | Description | AR-unn5 | AR-nnd5 | |
| 1 | GO:0097367 | MF | 5 | carbohydrate derivative binding | J1 | - |
| GO:0008144 | MF | 6 | drug binding | J1 | - | |
| GO:0017076 | MF | 6 | purine nucleotide binding | J1 | - | |
| GO:0032553 | MF | 6 | ribonucleotide binding | J1 | - | |
| GO:0030554 | MF | 7 | adenyl nucleotide binding | J1 | - | |
| GO:0032555 | MF | 7 | purine ribonucleotide binding | J1 | - | |
| GO:0035639 | MF | 7 | purine ribonucleoside triphosphate binding | J1 | - | |
| GO:0032559 | MF | 8 | adenyl ribonucleotide binding | J1 | - | |
| GO:0005524 | MF | 9 | ATP binding | J1 | - | |
| 2 | GO:0009893 | BP | 5 | positive regulation of metabolic process | J3,E | - |
| GO:0009891 | BP | 6 | positive regulation of biosynthetic process | J1,J3,D,E,L | - | |
| GO:0010604 | BP | 6 | positive regulation of macromolecule metabolic process | J1,J3,D,E,L | - | |
| GO:0051173 | BP | 6 | positive regulation of nitrogen compound metabolic process | J1,J3,D,E,L | - | |
| GO:0031325 | BP | 6 | positive regulation of cellular metabolic process | J3,E | - | |
| GO:0010557 | BP | 8 | positive regulation of macromolecule biosynthetic process | J1,J3,D,E,L | - | |
| GO:0031328 | BP | 8 | positive regulation of cellular biosynthetic process | J1,J3,D,E,L | - | |
| GO:0045935 | BP | 8 | positive regulation of nucleobase-containing compound metabolic process | J1,J3,D,E,L | - | |
| GO:0010628 | BP | 9 | positive regulation of gene expression | J1,J3,D,E,L | - | |
| GO:0051254 | BP | 9 | positive regulation of RNA metabolic process | J1,J3,D,E,L | - | |
| GO:1902680 | BP | 10 | positive regulation of RNA biosynthetic process | J1,J3,D,E,L | - | |
| GO:1903508 | BP | 11 | positive regulation of nucleic acid-templated transcription | J1,J3,D,E,L | - | |
| GO:0006366 | BP | 11 | transcription by RNA polymerase II | J3 | - | |
| GO:0045893 | BP | 12 | positive regulation of transcription, DNA-templated | J1,J3,D,E,L | - | |
| GO:0006357 | BP | 12 | regulation of transcription by RNA polymerase II | J3 | - | |
| GO:0045944 | BP | 13 | positive regulation of transcription by RNA polymerase II | J1,J3,D,E,L | - | |
| GO:0008289 | MF | 3 | lipid binding | J1,D,L | - | |
| GO:0001067 | MF | 5 | regulatory region nucleic acid binding | J1,J3,D,E,L | - | |
| GO:0003677 | MF | 5 | DNA binding | J1,D,E,L | - | |
| GO:0003690 | MF | 6 | double-stranded DNA binding | J1,J3,D,E,L | - | |
| GO:0044212 | MF | 6 | transcription regulatory region DNA binding | J1,J3,D,E,L | - | |
| GO:0140110 | MF | 6 | transcription regulator activity | J1,J3,D,E,L | - | |
| GO:1990837 | MF | 7 | sequence-specific double-stranded DNA binding | J1,J3,D,E,L | - | |
| GO:0001047 | MF | 8 | core promoter binding | J1,J3,D,E,L | - | |
| GO:0001046 | MF | 9 | core promoter sequence-specific DNA binding | J1,J3,D,E,L | - | |
| GO:0001228 | MF | 9 | DNA-binding transcription activator activity, RNA polymerase II-specific | J1,J3,D,E,L | - | |
| GO:0003700 | MF | 11 | DNA-binding transcription factor activity | J1,J3,D,E,L | - | |
| GO:0000976 | MF | 14 | transcription regulatory region sequence-specific DNA binding | J1,J3,D,E,L | - | |
| GO:0000981 | MF | 15 | DNA-binding transcription factor activity, RNA polymerase II-specific | J1,J3,D,E,L | - | |
| 3 | GO:0009987 | BP | 2 | cellular process | J1,J3,D,E,L | J1,J3,D,E,L |
| GO:0006807 | BP | 3 | nitrogen compound metabolic process | J1,D,E | - | |
| GO:0071704 | BP | 3 | organic substance metabolic process | J1,D,E | J1,J3,D,E,L | |
| GO:0044238 | BP | 4 | primary metabolic process | J1,J3,D,E | J1,J3,D,E,L | |
| GO:0044237 | BP | 4 | cellular metabolic process | J1,J3,D,E | J3,L | |
| GO:0044260 | BP | 5 | cellular macromolecule metabolic process | J1,D,E | - | |
| GO:0043412 | BP | 5 | macromolecule modification | J1,J3,D,E | J3,L | |
| GO:0044267 | BP | 6 | cellular protein metabolic process | J1,D,E | J3,L | |
| GO:0036211 | BP | 6 | protein modification process | J1,J3,D,E | J3,L | |
| GO:0006464 | BP | 7 | cellular protein modification process | J1,J3,D,E | J3,L | |
| GO:0016020 | CC | 3 | membrane | J1,J3,L | J1,J3,D,E,L | |
| GO:0071944 | CC | 4 | cell periphery | J1,J3,D,E,L | J1,J3,D,E,L | |
| GO:0005886 | CC | 5 | plasma membrane | J1,J3,D,E,L | J1,J3,D,E,L | |
| GO:0005488 | MF | 2 | binding | J1,J3,D,E,L | J1,J3,D,E,L | |
| GO:0016740 | MF | 3 | transferase activity | J1,E,L | J1,J3,D,E,L | |
| GO:0097159 | MF | 3 | organic cyclic compound binding | J1,J3,D,E,L | J1,J3,D,E,L | |
| GO:1901363 | MF | 3 | heterocyclic compound binding | J1,J3,D,E,L | J1,J3,D,E,L | |
| GO:0016772 | MF | 4 | transferase activity, transferring phosphorus-containing groups | J1,J3,D,L | J1,J3,D,E,L | |
| GO:0016301 | MF | 5 | kinase activity | J1,J3,D,L | J1,J3,D,E,L | |
| 4 | GO:0008152 | BP | 2 | metabolic process | - | J1,J3,D,E,L |
| GO:0050896 | BP | 2 | response to stimulus | - | J1,J3,D,E,L | |
| GO:0009056 | BP | 3 | catabolic process | - | J1,J3,D,E,L | |
| GO:0009058 | BP | 3 | biosynthetic process | - | J1,J3,D,E,L | |
| GO:0009719 | BP | 3 | response to endogenous stimulus | - | J1,J3,D,E,L | |
| GO:0019748 | BP | 3 | secondary metabolic process | - | J1,J3,D,E,L | |
| GO:0005975 | BP | 4 | carbohydrate metabolic process | - | J1,J3,D,E,L | |
| GO:0006091 | BP | 4 | generation of precursor metabolites and energy | - | J1,J3,D,E,L | |
| GO:0006629 | BP | 4 | lipid metabolic process | - | J1,J3,D,E,L | |
| GO:0015979 | BP | 4 | photosynthesis | - | J1,J3,D,E,L | |
| GO:1901564 | BP | 4 | organonitrogen compound metabolic process | - | J3 | |
| GO:0019538 | BP | 5 | protein metabolic process | - | J3 | |
| GO:0005576 | CC | 2 | extracellular region | - | J1,J3,D,E,L | |
| GO:0005623 | CC | 2 | cell | - | J1,J3,D,E,L | |
| GO:0043226 | CC | 2 | organelle | - | J3,D | |
| GO:0044464 | CC | 3 | cell part | - | J1,J3,D,E,L | |
| GO:0030312 | CC | 5 | external encapsulating structure | - | J1,J3,D,E,L | |
| GO:0043227 | CC | 5 | membrane-bounded organelle | - | J3,D | |
| GO:0005737 | CC | 6 | cytoplasm | - | D | |
| GO:0005618 | CC | 6 | cell wall | - | J1,J3,D,E,L | |
| GO:0009579 | CC | 6 | thylakoid | - | J1,J3,D,E,L | |
| GO:0043229 | CC | 6 | intracellular organelle | - | J3,D | |
| GO:0012505 | CC | 6 | endomembrane system | - | J3,D,E | |
| GO:0043231 | CC | 7 | intracellular membrane-bounded organelle | - | J3,D | |
| GO:0044444 | CC | 7 | cytoplasmic part | - | J3,D | |
| GO:0005794 | CC | 8 | Golgi apparatus | - | J1,D,E | |
| GO:0009536 | CC | 8 | plastid | - | J1,J3,D,E,L | |
| GO:0003824 | MF | 2 | catalytic activity | - | J1,J3,D,E,L | |
| GO:0005215 | MF | 2 | transporter activity | - | J1,J3,D,E,L | |
| GO:0016787 | MF | 3 | hydrolase activity | - | J1,J3,D,E,L | |
| GO:0030246 | MF | 3 | carbohydrate binding | - | J1,J3,D,E,L | |
| GO:0036094 | MF | 4 | small molecule binding | - | J1,J3,D,E,L | |
| GO:1901265 | MF | 4 | nucleoside phosphate binding | - | J1,J3,D,E,L | |
| GO:0000166 | MF | 5 | nucleotide binding | - | J1,J3,D,E,L | |
1Only Groups 1–4 are shown. Full details on all Groups 5–8 are given in S3 Table
2Analysis methods identifying significant DEGs associated with the indicated enriched GO term and expression category. D = DESeq2, E = edgeR and L = limma-voom.
3MF = Molecular Function; BP = Biological Process; CC = Cellular component.
4Ascending numbers indicate a more specific category in the GO terms hierarchies.
5Abbreviated expression categories. u = up; d = down; n = ns.