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Table 2 Significantly enriched GO terms (Biological Process Ontology) in the subsets of differentially expressed genes (p-value < 0.05)

From: Transcriptional reprogramming caused by the geminivirus Tomato yellow leaf curl virus in local or systemic infections in Nicotiana benthamiana

GO.ID Term Annotated Significant Expected p-value
Overrepresented in the subset of up-regulated in local infection
 GO:0006351 transcription, DNA-templated 2046 271 151.48 1.8E-22
 GO:0006310 DNA recombination 47 15 3.48 2.5E-06
 GO:0005992 trehalose biosynthetic process 34 12 2.52 3.1E-06
 GO:0048544 recognition of pollen 69 16 5.11 0.000034
 GO:0006302 double-strand break repair 16 7 1.18 0.000076
 GO:0006464 cellular protein modification process 2490 237 184.35 0.00008
 GO:0006012 galactose metabolic process 23 8 1.7 0.00016
 GO:0006950 response to stress 873 108 64.63 0.00022
 GO:0016310 phosphorylation 2148 196 159.03 0.00023
 GO:0006376 mRNA splice site selection 6 4 0.44 0.0004
 GO:0032968 positive regulation of transcription elongation from RNA polymerase II promoter 3 3 0.22 0.00041
 GO:0006887 exocytosis 72 14 5.33 0.00071
 GO:0006635 fatty acid beta-oxidation 7 4 0.52 0.00087
 GO:0006281 DNA repair 271 38 20.06 0.00415
 GO:0043562 cellular response to nitrogen levels 2 2 0.15 0.00548
 GO:0009744 response to sucrose 2 2 0.15 0.00548
 GO:0045454 cell redox homeostasis 229 28 16.95 0.00608
 GO:0008272 sulfate transport 31 7 2.3 0.00653
 GO:0000160 phosphorelay signal transduction system 102 15 7.55 0.00799
 GO:0006334 nucleosome assembly 59 10 4.37 0.01074
 GO:0009298 GDP-mannose biosynthetic process 7 3 0.52 0.0113
 GO:0070966 nuclear-transcribed mRNA catabolic process, no-go decay 3 2 0.22 0.01562
 GO:0070481 nuclear-transcribed mRNA catabolic process, non-stop decay 3 2 0.22 0.01562
 GO:0071025 RNA surveillance 3 2 0.22 0.01562
 GO:0015706 nitrate transport 3 2 0.22 0.01562
 GO:0010167 response to nitrate 3 2 0.22 0.01562
 GO:0007064 mitotic sister chromatid cohesion 8 3 0.59 0.01709
 GO:0006032 chitin catabolic process 31 6 2.3 0.02419
 GO:0035434 copper ion transmembrane transport 9 3 0.67 0.02425
 GO:0050832 defense response to fungus 4 2 0.3 0.02972
 GO:0042742 defense response to bacterium 4 2 0.3 0.02972
 GO:0007050 cell cycle arrest 10 3 0.74 0.03277
 GO:0006529 asparagine biosynthetic process 11 3 0.81 0.04263
 GO:0006020 inositol metabolic process 11 3 0.81 0.04263
Overrepresented in the subset of down-regulated in local infection
 GO:0009765 photosynthesis, light harvesting 74 61 12.92 1E-30
 GO:0007017 microtubule-based process 254 105 44.35 4.6E-19
 GO:0033014 tetrapyrrole biosynthetic process 53 32 9.25 3.3E-12
 GO:0015979 photosynthesis 387 169 67.57 4.9E-12
 GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity 48 29 8.38 3.4E-11
 GO:0006270 DNA replication initiation 18 16 3.14 7.7E-11
 GO:0072330 monocarboxylic acid biosynthetic process 171 61 29.85 8.1E-09
 GO:0051258 protein polymerization 86 34 15.01 8.8E-09
 GO:0006546 glycine catabolic process 11 9 1.92 5.8E-06
 GO:0005975 carbohydrate metabolic process 1345 320 234.82 0.000013
 GO:0006073 cellular glucan metabolic process 142 56 24.79 0.000026
 GO:0006260 DNA replication 119 55 20.78 0.000027
 GO:0000910 cytokinesis 24 12 4.19 0.000033
 GO:0006629 lipid metabolic process 928 234 162.02 0.00028
 GO:0030244 cellulose biosynthetic process 62 22 10.82 0.00051
 GO:0000096 sulfur amino acid metabolic process 50 18 8.73 0.00084
 GO:0006656 phosphatidylcholine biosynthetic process 4 4 0.7 0.00093
 GO:0018160 peptidyl-pyrromethane cofactor linkage 4 4 0.7 0.00093
 GO:1901070 guanosine-containing compound biosynthetic process 17 9 2.97 0.00094
 GO:0006418 tRNA aminoacylation for protein translation 95 29 16.59 0.00125
 GO:0009132 nucleoside diphosphate metabolic process 135 40 23.57 0.00155
 GO:0006228 UTP biosynthetic process 15 8 2.62 0.00171
 GO:0006241 CTP biosynthetic process 15 8 2.62 0.00171
 GO:0006269 DNA replication, synthesis of RNA primer 5 4 0.87 0.00399
 GO:0045132 meiotic chromosome segregation 5 4 0.87 0.00399
 GO:0009084 glutamine family amino acid biosynthetic process 31 12 5.41 0.00416
 GO:1901617 organic hydroxy compound biosynthetic process 23 14 4.02 0.00531
 GO:0009234 menaquinone biosynthetic process 3 3 0.52 0.00532
 GO:0016117 carotenoid biosynthetic process 14 7 2.44 0.00536
 GO:0009065 glutamine family amino acid catabolic process 12 6 2.1 0.00997
 GO:0046168 glycerol-3-phosphate catabolic process 6 4 1.05 0.01031
 GO:0015671 oxygen transport 6 4 1.05 0.01031
 GO:0006801 superoxide metabolic process 23 9 4.02 0.01161
 GO:0007076 mitotic chromosome condensation 13 6 2.27 0.01582
 GO:0006166 purine ribonucleoside salvage 4 3 0.7 0.01849
 GO:0006096 glycolytic process 114 29 19.9 0.02014
 GO:0046274 lignin catabolic process 33 11 5.76 0.02045
 GO:0042549 photosystem II stabilization 7 4 1.22 0.02075
 GO:0042026 protein refolding 14 6 2.44 0.02366
 GO:0019307 mannose biosynthetic process 2 2 0.35 0.03047
 GO:0007155 cell adhesion 2 2 0.35 0.03047
 GO:0045038 protein import into chloroplast thylakoid membrane 2 2 0.35 0.03047
 GO:0048478 replication fork protection 2 2 0.35 0.03047
 GO:0007623 circadian rhythm 2 2 0.35 0.03047
 GO:0010027 thylakoid membrane organization 2 2 0.35 0.03047
 GO:0006450 regulation of translational fidelity 2 2 0.35 0.03047
 GO:0030259 lipid glycosylation 15 6 2.62 0.03373
 GO:0009082 branched-chain amino acid biosynthetic process 23 8 4.02 0.03537
 GO:0006168 adenine salvage 5 3 0.87 0.04023
 GO:0010207 photosystem II assembly 5 3 0.87 0.04023
 GO:0006353 DNA-templated transcription, termination 5 3 0.87 0.04023
 GO:0006662 glycerol ether metabolic process 68 18 11.87 0.04094
Overrepresented in the subset of up-regulated in systemic infection
 GO:0006032 chitin catabolic process 31 7 0.78 9.1E-06
 GO:0006355 regulation of transcription, DNA-templated 1764 69 44.11 0.00012
 GO:0005975 carbohydrate metabolic process 1345 63 33.64 0.00022
 GO:0043562 cellular response to nitrogen levels 2 2 0.05 0.00062
 GO:0009744 response to sucrose 2 2 0.05 0.00062
 GO:0016998 cell wall macromolecule catabolic process 29 5 0.73 0.00069
 GO:0019310 inositol catabolic process 8 3 0.2 0.00079
 GO:0005992 trehalose biosynthetic process 34 5 0.85 0.00146
 GO:0015770 sucrose transport 3 2 0.08 0.00184
 GO:0019953 sexual reproduction 11 3 0.28 0.00221
 GO:0009607 response to biotic stimulus 43 6 1.08 0.00271
 GO:0006570 tyrosine metabolic process 5 2 0.13 0.00594
 GO:0006094 gluconeogenesis 8 2 0.2 0.01581
 GO:0006952 defense response 112 8 2.8 0.01862
 GO:0006541 glutamine metabolic process 23 3 0.58 0.01898
 GO:0000272 polysaccharide catabolic process 25 3 0.63 0.02376
 GO:0006662 glycerol ether metabolic process 68 5 1.7 0.02756
 GO:0003333 amino acid transmembrane transport 46 4 1.15 0.02758
 GO:0006529 asparagine biosynthetic process 11 2 0.28 0.02956
 GO:0008283 cell proliferation 11 2 0.28 0.02956
 GO:0044264 cellular polysaccharide metabolic process 148 7 3.7 0.03961
 GO:0008272 sulfate transport 31 3 0.78 0.04163
 GO:0006857 oligopeptide transport 33 3 0.83 0.04874
Overrepresented in the subset of down-regulated in systemic infection
 GO:0007018 microtubule-based movement 129 11 0.7 1.2E-10
 GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity 48 7 0.26 7.2E-09
 GO:0007067 mitotic nuclear division 51 5 0.28 0.0001
 GO:0016114 terpenoid biosynthetic process 30 2 0.16 0.0116
 GO:0006265 DNA topological change 30 2 0.16 0.0116
 GO:0007094 mitotic spindle assembly checkpoint 3 1 0.02 0.0163
 GO:0006952 defense response 112 3 0.61 0.0235
 GO:0009813 flavonoid biosynthetic process 6 1 0.03 0.0323
 GO:0030244 cellulose biosynthetic process 62 2 0.34 0.0452
Overrepresented in the subset of up-regulated genes common to local and systemic infections
 GO:0043562 cellular response to nitrogen levels 2 2 0.01 0.000041
 GO:0009744 response to sucrose 2 2 0.01 0.000041
 GO:0005992 trehalose biosynthetic process 34 4 0.22 0.000066
 GO:0006094 gluconeogenesis 8 2 0.05 0.0011
 GO:0019310 inositol catabolic process 8 2 0.05 0.0011
 GO:0006529 asparagine biosynthetic process 11 2 0.07 0.0022
 GO:0006355 regulation of transcription, DNA-templated 1764 21 11.37 0.0043
 GO:0007205 protein kinase C-activating G-protein coupled receptor signaling pathway 24 2 0.15 0.0104
 GO:0006659 phosphatidylserine biosynthetic process 3 1 0.02 0.0192
 GO:0042742 defense response to bacterium 4 1 0.03 0.0255
 GO:0006562 proline catabolic process 4 1 0.03 0.0255
 GO:0050832 defense response to fungus 4 1 0.03 0.0255
 GO:0006570 tyrosine metabolic process 5 1 0.03 0.0318
 GO:0003333 amino acid transmembrane transport 46 2 0.3 0.0355
 GO:0009064 glutamine family amino acid metabolic process 57 3 0.37 0.0453
Overrepresented in the subset of down-regulated genes common to local and systemic infections
 GO:0007018 microtubule-based movement 129 10 0.43 1.4E-11
 GO:0000079 regulation of cyclin-dependent protein serine/threonine kinase activity 48 7 0.16 2.1E-10
 GO:0007067 mitotic nuclear division 51 5 0.17 0.000014
 GO:0006265 DNA topological change 30 2 0.1 0.0045
 GO:0007094 mitotic spindle assembly checkpoint 3 1 0.01 0.0099
 GO:0030244 cellulose biosynthetic process 62 2 0.21 0.0181
 GO:0006606 protein import into nucleus 12 1 0.04 0.0392