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Table 2 GO function analysis of the enriched differential methylated genes

From: Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in Maize (Zea may)

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