Table 2.
GO function analysis of the enriched differential methylated genes
| Category | GO term | Count | P-value |
|---|---|---|---|
| biological process | |||
| GO:0015979 | photosynthesis | 224 | 9.30E-13 |
| GO:0022900 | electron transport chain | 232 | 2.13E-11 |
| GO:0022904 | respiratory electron transport chain | 98 | 5.01E-10 |
| GO:0006091 | generation of precursor metabolites and energy | 384 | 9.60E-10 |
| GO:0006119 | oxidative phosphorylation | 89 | 1.29E-08 |
| GO:0042773 | ATP synthesis coupled electron transport | 89 | 1.29E-08 |
| GO:0015980 | energy derivation by oxidation of organic compounds | 142 | 1.39E-07 |
| GO:0045333 | cellular respiration | 135 | 1.67E-07 |
| GO:0019684 | photosynthesis, light reaction | 140 | 2.64E-07 |
| GO:0009767 | photosynthetic electron transport chain | 59 | 2.87E-07 |
| GO:0009772 | photosynthetic electron transport in photosystem II | 25 | 2.79E-06 |
| GO:0044237 | cellular metabolic process | 3685 | 5.18E-06 |
| GO:0009058 | biosynthetic process | 1708 | 7.56E-06 |
| GO:0044249 | cellular biosynthetic process | 1597 | 3.61E-05 |
| GO:0009987 | cellular process | 4664 | 0.00011 |
| GO:0015985 | energy coupled proton transport, down electrochemical gradient | 46 | 0.00014 |
| GO:0015986 | ATP synthesis coupled proton transport | 46 | 0.00014 |
| GO:0042777 | plasma membrane ATP synthesis coupled proton transport | 18 | 0.00016 |
| GO:0006351 | transcription, DNA-dependent | 206 | 0.00017 |
| GO:0032774 | RNA biosynthetic process | 207 | 0.00032 |
| GO:0009145 | purine nucleoside triphosphate biosynthetic process | 69 | 0.00033 |
| GO:0009206 | purine ribonucleoside triphosphate biosynthetic process | 69 | 0.00033 |
| GO:0034645 | cellular macromolecule biosynthetic process | 940 | 0.00035 |
| GO:0009059 | macromolecule biosynthetic process | 947 | 0.00093 |
| GO:0009201 | ribonucleoside triphosphate biosynthetic process | 70 | 0.00185 |
| GO:0009142 | nucleoside triphosphate biosynthetic process | 72 | 0.00189 |
| GO:0015672 | monovalent inorganic cation transport | 142 | 0.00216 |
| GO:0009152 | purine ribonucleotide biosynthetic process | 81 | 0.00222 |
| GO:0006818 | hydrogen transport | 77 | 0.00226 |
| GO:0015992 | proton transport | 77 | 0.00226 |
| GO:0042775 | mitochondrial ATP synthesis coupled electron transport | 56 | 0.00272 |
| GO:0006754 | ATP biosynthetic process | 63 | 0.00586 |
| GO:0006164 | purine nucleotide biosynthetic process | 84 | 0.01066 |
| GO:0006120 | mitochondrial electron transport, NADH to ubiquinone | 38 | 0.01086 |
| GO:0010467 | gene expression | 846 | 0.01137 |
| GO:0072522 | purine-containing compound biosynthetic process | 88 | 0.01641 |
| GO:0008152 | metabolic process | 4538 | 0.01879 |
| cellular component | |||
| GO:0009507 | chloroplast | 1513 | 2.21E-14 |
| GO:0034357 | photosynthetic membrane | 277 | 9.70E-14 |
| GO:0044436 | thylakoid part | 289 | 1.13E-13 |
| GO:0042651 | thylakoid membrane | 268 | 1.87E-13 |
| GO:0055035 | plastid thylakoid membrane | 263 | 2.47E-13 |
| GO:0009535 | chloroplast thylakoid membrane | 262 | 3.82E-13 |
| GO:0009534 | chloroplast thylakoid | 290 | 7.41E-13 |
| GO:0031976 | plastid thylakoid | 290 | 7.41E-13 |
| GO:0009579 | thylakoid | 345 | 4.30E-12 |
| GO:0031984 | organelle subcompartment | 294 | 4.46E-12 |
| GO:0009539 | photosystem II reaction center | 20 | 2.60E-08 |
| GO:0009536 | plastid | 2256 | 7.71E-07 |
| GO:0009523 | photosystem II | 62 | 1.57E-06 |
| GO:0009521 | photosystem | 74 | 1.78E-06 |
| GO:0030076 | light-harvesting complex | 22 | 9.18E-06 |
| GO:0044422 | organelle part | 1690 | 1.14E-05 |
| GO:0044446 | intracellular organelle part | 1686 | 1.25E-05 |
| GO:0033177 | proton-transporting two-sector ATPase complex, proton-transporting domain | 34 | 1.40E-05 |
| GO:0032991 | macromolecular complex | 1156 | 2.06E-05 |
| GO:0045263 | proton-transporting ATP synthase complex, coupling factor F(o) | 27 | 2.74E-05 |
| GO:0005761 | mitochondrial ribosome | 41 | 3.68E-05 |
| GO:0045259 | proton-transporting ATP synthase complex | 43 | 5.44E-05 |
| GO:0016469 | proton-transporting two-sector ATPase complex | 57 | 6.01E-05 |
| GO:0005840 | ribosome | 337 | 0.00012 |
| GO:0044434 | chloroplast part | 663 | 0.00018 |
| GO:0044429 | mitochondrial part | 220 | 0.00049 |
| GO:0044391 | ribosomal subunit | 179 | 0.00068 |
| GO:0044435 | plastid part | 671 | 0.00069 |
| GO:0005762 | mitochondrial large ribosomal subunit | 14 | 0.00184 |
| GO:0005739 | mitochondrion | 1597 | 0.00213 |
| GO:0043234 | protein complex | 769 | 0.00294 |
| GO:0000313 | organellar ribosome | 41 | 0.00436 |
| GO:0005759 | mitochondrial matrix | 70 | 0.00484 |
| GO:0015935 | small ribosomal subunit | 88 | 0.01036 |
| GO:0030075 | plasma membrane-derived thylakoid | 9 | 0.01078 |
| GO:0030096 | plasma membrane-derived thylakoid photosystem II | 9 | 0.01078 |
| GO:0030529 | ribonucleoprotein complex | 394 | 0.01593 |
| GO:0005753 | mitochondrial proton-transporting ATP synthase complex | 29 | 0.01639 |
| GO:0016021 | integral to membrane | 882 | 0.03048 |
| GO:0044425 | membrane part | 1118 | 0.03143 |
| GO:0044444 | cytoplasmic part | 5004 | 0.03237 |
| molecular function | |||
| GO:0048038 | quinone binding | 69 | 1.29E-10 |
| GO:0050136 | NADH dehydrogenase (quinone) activity | 86 | 2.42E-10 |
| GO:0008137 | NADH dehydrogenase (ubiquinone) activity | 82 | 2.07E-09 |
| GO:0003954 | NADH dehydrogenase activity | 86 | 6.51E-09 |
| GO:0019843 | rRNA binding | 92 | 3.35E-08 |
| GO:0003899 | DNA-directed RNA polymerase activity | 93 | 4.58E-08 |
| GO:0034062 | RNA polymerase activity | 95 | 8.32E-08 |
| GO:0016655 | oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor | 91 | 5.39E-07 |
| GO:0016651 | oxidoreductase activity, acting on NADH or NADPH | 117 | 5.94E-06 |
| GO:0045156 | electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity | 25 | 2.61E-05 |
| GO:0005198 | structural molecule activity | 325 | 0.00023 |
| GO:0046933 | hydrogen ion transporting ATP synthase activity, rotational mechanism | 34 | 0.00055 |
| GO:0003735 | structural constituent of ribosome | 254 | 0.00058 |
| GO:0032549 | ribonucleoside binding | 31 | 0.00065 |
| GO:0001882 | nucleoside binding | 31 | 0.00135 |
| GO:0015078 | hydrogen ion transmembrane transporter activity | 99 | 0.00302 |
| GO:0015077 | monovalent inorganic cation transmembrane transporter activity | 134 | 0.00421 |
| GO:0016779 | nucleotidyltransferase activity | 200 | 0.00936 |
| GO:0016984 | ribulose-bisphosphate carboxylase activity | 18 | 0.04269 |