Gene type: Transcription factor Metabolic gene Others DE type: Up Down Slightly_up Slightly_down Mixeded Others

GO Enrichment Analysis of Co-expressed Genes with

AT3G25480

GO-BP
GO-MF
GO-CC
RankGO TermAdjusted P value
1GO:0032194: ubiquinone biosynthetic process via 3,4-dihydroxy-5-polyprenylbenzoate0.00E+00
2GO:0090071: negative regulation of ribosome biogenesis0.00E+00
3GO:0006223: uracil salvage0.00E+00
4GO:0042821: pyridoxal biosynthetic process0.00E+00
5GO:0070272: proton-transporting ATP synthase complex biogenesis0.00E+00
6GO:0097164: ammonium ion metabolic process0.00E+00
7GO:0042820: vitamin B6 catabolic process0.00E+00
8GO:1905499: trichome papilla formation0.00E+00
9GO:0006399: tRNA metabolic process0.00E+00
10GO:0018160: peptidyl-pyrromethane cofactor linkage0.00E+00
11GO:0015995: chlorophyll biosynthetic process7.83E-13
12GO:0032544: plastid translation5.80E-10
13GO:0006782: protoporphyrinogen IX biosynthetic process3.02E-07
14GO:0009658: chloroplast organization4.47E-07
15GO:0006412: translation9.73E-07
16GO:0010027: thylakoid membrane organization1.56E-06
17GO:0015979: photosynthesis1.69E-06
18GO:1901259: chloroplast rRNA processing2.15E-06
19GO:0009735: response to cytokinin2.88E-06
20GO:0008616: queuosine biosynthetic process3.02E-06
21GO:0006783: heme biosynthetic process1.07E-05
22GO:0090391: granum assembly1.09E-05
23GO:0006779: porphyrin-containing compound biosynthetic process1.45E-05
24GO:0051085: chaperone mediated protein folding requiring cofactor2.46E-05
25GO:0006353: DNA-templated transcription, termination2.38E-04
26GO:0019354: siroheme biosynthetic process2.55E-04
27GO:0009443: pyridoxal 5'-phosphate salvage2.55E-04
28GO:1904966: positive regulation of vitamin E biosynthetic process2.55E-04
29GO:1904964: positive regulation of phytol biosynthetic process2.55E-04
30GO:0042371: vitamin K biosynthetic process2.55E-04
31GO:0043686: co-translational protein modification2.55E-04
32GO:0006436: tryptophanyl-tRNA aminoacylation2.55E-04
33GO:1902458: positive regulation of stomatal opening2.55E-04
34GO:0034337: RNA folding2.55E-04
35GO:0042254: ribosome biogenesis4.07E-04
36GO:0007000: nucleolus organization5.64E-04
37GO:1902326: positive regulation of chlorophyll biosynthetic process5.64E-04
38GO:0070981: L-asparagine biosynthetic process5.64E-04
39GO:0080183: response to photooxidative stress5.64E-04
40GO:0006529: asparagine biosynthetic process5.64E-04
41GO:0006729: tetrahydrobiopterin biosynthetic process5.64E-04
42GO:1903426: regulation of reactive oxygen species biosynthetic process5.64E-04
43GO:0006568: tryptophan metabolic process5.64E-04
44GO:0045037: protein import into chloroplast stroma6.51E-04
45GO:0010207: photosystem II assembly8.30E-04
46GO:0006633: fatty acid biosynthetic process8.88E-04
47GO:0051211: anisotropic cell growth9.15E-04
48GO:0000280: nuclear division9.15E-04
49GO:0006518: peptide metabolic process9.15E-04
50GO:0051604: protein maturation9.15E-04
51GO:0071492: cellular response to UV-A9.15E-04
52GO:0006760: folic acid-containing compound metabolic process9.15E-04
53GO:0019344: cysteine biosynthetic process1.14E-03
54GO:0006241: CTP biosynthetic process1.31E-03
55GO:0009052: pentose-phosphate shunt, non-oxidative branch1.31E-03
56GO:0006165: nucleoside diphosphate phosphorylation1.31E-03
57GO:0006228: UTP biosynthetic process1.31E-03
58GO:0050482: arachidonic acid secretion1.31E-03
59GO:0006986: response to unfolded protein1.31E-03
60GO:0080158: chloroplast ribulose bisphosphate carboxylase complex biogenesis1.31E-03
61GO:2001141: regulation of RNA biosynthetic process1.31E-03
62GO:0006457: protein folding1.34E-03
63GO:0006183: GTP biosynthetic process1.75E-03
64GO:0046656: folic acid biosynthetic process1.75E-03
65GO:0030007: cellular potassium ion homeostasis1.75E-03
66GO:0044206: UMP salvage1.75E-03
67GO:0006021: inositol biosynthetic process1.75E-03
68GO:0071486: cellular response to high light intensity1.75E-03
69GO:0042335: cuticle development2.07E-03
70GO:0006665: sphingolipid metabolic process2.23E-03
71GO:0043097: pyrimidine nucleoside salvage2.23E-03
72GO:0010236: plastoquinone biosynthetic process2.23E-03
73GO:0045038: protein import into chloroplast thylakoid membrane2.23E-03
74GO:0031365: N-terminal protein amino acid modification2.23E-03
75GO:0006655: phosphatidylglycerol biosynthetic process2.75E-03
76GO:0010190: cytochrome b6f complex assembly2.75E-03
77GO:0006206: pyrimidine nucleobase metabolic process2.75E-03
78GO:0006086: acetyl-CoA biosynthetic process from pyruvate2.75E-03
79GO:0007035: vacuolar acidification2.75E-03
80GO:0009117: nucleotide metabolic process2.75E-03
81GO:0046855: inositol phosphate dephosphorylation2.75E-03
82GO:0032502: developmental process2.94E-03
83GO:0009955: adaxial/abaxial pattern specification3.30E-03
84GO:0042372: phylloquinone biosynthetic process3.30E-03
85GO:0042026: protein refolding3.30E-03
86GO:0017148: negative regulation of translation3.30E-03
87GO:0046654: tetrahydrofolate biosynthetic process3.30E-03
88GO:0010019: chloroplast-nucleus signaling pathway3.30E-03
89GO:0010555: response to mannitol3.30E-03
90GO:0045454: cell redox homeostasis3.61E-03
91GO:0009772: photosynthetic electron transport in photosystem II3.89E-03
92GO:0010196: nonphotochemical quenching3.89E-03
93GO:0006826: iron ion transport3.89E-03
94GO:0009627: systemic acquired resistance4.44E-03
95GO:0006644: phospholipid metabolic process4.52E-03
96GO:0048564: photosystem I assembly4.52E-03
97GO:0009642: response to light intensity4.52E-03
98GO:0042255: ribosome assembly4.52E-03
99GO:0006875: cellular metal ion homeostasis4.52E-03
100GO:2000070: regulation of response to water deprivation4.52E-03
101GO:0071482: cellular response to light stimulus5.18E-03
102GO:0015996: chlorophyll catabolic process5.18E-03
103GO:0007186: G-protein coupled receptor signaling pathway5.18E-03
104GO:0009657: plastid organization5.18E-03
105GO:0017004: cytochrome complex assembly5.18E-03
106GO:0009245: lipid A biosynthetic process5.86E-03
107GO:0034765: regulation of ion transmembrane transport5.86E-03
108GO:0042761: very long-chain fatty acid biosynthetic process6.58E-03
109GO:0031425: chloroplast RNA processing6.58E-03
110GO:0006535: cysteine biosynthetic process from serine7.33E-03
111GO:0045036: protein targeting to chloroplast7.33E-03
112GO:0043085: positive regulation of catalytic activity8.11E-03
113GO:0006415: translational termination8.11E-03
114GO:0006352: DNA-templated transcription, initiation8.11E-03
115GO:0006790: sulfur compound metabolic process8.92E-03
116GO:0016024: CDP-diacylglycerol biosynthetic process8.92E-03
117GO:0042538: hyperosmotic salinity response1.06E-02
118GO:0006541: glutamine metabolic process1.06E-02
119GO:0010020: chloroplast fission1.06E-02
120GO:0010167: response to nitrate1.15E-02
121GO:0019853: L-ascorbic acid biosynthetic process1.15E-02
122GO:0010039: response to iron ion1.15E-02
123GO:0046854: phosphatidylinositol phosphorylation1.15E-02
124GO:0010025: wax biosynthetic process1.24E-02
125GO:0080167: response to karrikin1.26E-02
126GO:0009116: nucleoside metabolic process1.34E-02
127GO:0000027: ribosomal large subunit assembly1.34E-02
128GO:0006418: tRNA aminoacylation for protein translation1.43E-02
129GO:0043622: cortical microtubule organization1.43E-02
130GO:0007017: microtubule-based process1.43E-02
131GO:0061077: chaperone-mediated protein folding1.53E-02
132GO:0015992: proton transport1.53E-02
133GO:0051260: protein homooligomerization1.53E-02
134GO:0007005: mitochondrion organization1.64E-02
135GO:0009411: response to UV1.74E-02
136GO:0010091: trichome branching1.85E-02
137GO:0016117: carotenoid biosynthetic process1.95E-02
138GO:0000413: protein peptidyl-prolyl isomerization2.07E-02
139GO:0006662: glycerol ether metabolic process2.18E-02
140GO:0010182: sugar mediated signaling pathway2.18E-02
141GO:0009741: response to brassinosteroid2.18E-02
142GO:0009646: response to absence of light2.29E-02
143GO:0008152: metabolic process2.33E-02
144GO:0009790: embryo development2.39E-02
145GO:0008654: phospholipid biosynthetic process2.41E-02
146GO:0009567: double fertilization forming a zygote and endosperm2.90E-02
147GO:0010286: heat acclimation3.03E-02
148GO:0071805: potassium ion transmembrane transport3.03E-02
149GO:0000910: cytokinesis3.16E-02
150GO:0008380: RNA splicing3.37E-02
151GO:0010029: regulation of seed germination3.42E-02
152GO:0042128: nitrate assimilation3.56E-02
153GO:0009817: defense response to fungus, incompatible interaction3.97E-02
154GO:0048481: plant ovule development3.97E-02
155GO:0018298: protein-chromophore linkage3.97E-02
156GO:0008219: cell death3.97E-02
157GO:0010119: regulation of stomatal movement4.41E-02
158GO:0009637: response to blue light4.70E-02
159GO:0015031: protein transport4.78E-02
160GO:0034599: cellular response to oxidative stress4.85E-02
RankGO TermAdjusted P value
1GO:0009974: zeinoxanthin epsilon hydroxylase activity0.00E+00
2GO:0033728: divinyl chlorophyllide a 8-vinyl-reductase activity0.00E+00
3GO:0047450: crotonoyl-[acyl-carrier-protein] hydratase activity0.00E+00
4GO:0050236: pyridoxine:NADP 4-dehydrogenase activity0.00E+00
5GO:0015269: calcium-activated potassium channel activity0.00E+00
6GO:0000979: RNA polymerase II core promoter sequence-specific DNA binding0.00E+00
7GO:0004851: uroporphyrin-III C-methyltransferase activity0.00E+00
8GO:0048307: ferredoxin-nitrite reductase activity0.00E+00
9GO:0051744: 3,8-divinyl protochlorophyllide a 8-vinyl reductase activity0.00E+00
10GO:0046428: 1,4-dihydroxy-2-naphthoate octaprenyltransferase activity0.00E+00
11GO:0004853: uroporphyrinogen decarboxylase activity0.00E+00
12GO:0019166: trans-2-enoyl-CoA reductase (NADPH) activity0.00E+00
13GO:0050421: nitrite reductase (NO-forming) activity0.00E+00
14GO:0004418: hydroxymethylbilane synthase activity0.00E+00
15GO:0004314: [acyl-carrier-protein] S-malonyltransferase activity0.00E+00
16GO:0015038: glutathione disulfide oxidoreductase activity0.00E+00
17GO:0046408: chlorophyll synthetase activity0.00E+00
18GO:0047889: ferredoxin-nitrate reductase activity0.00E+00
19GO:0019843: rRNA binding4.48E-07
20GO:0003735: structural constituent of ribosome7.74E-07
21GO:0008479: queuine tRNA-ribosyltransferase activity3.02E-06
22GO:0016851: magnesium chelatase activity2.46E-05
23GO:0003755: peptidyl-prolyl cis-trans isomerase activity1.98E-04
24GO:0030794: (S)-coclaurine-N-methyltransferase activity2.55E-04
25GO:0004425: indole-3-glycerol-phosphate synthase activity2.55E-04
26GO:0004560: alpha-L-fucosidase activity2.55E-04
27GO:0050567: glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity2.55E-04
28GO:0004071: aspartate-ammonia ligase activity2.55E-04
29GO:0009374: biotin binding2.55E-04
30GO:0042586: peptide deformylase activity2.55E-04
31GO:0008124: 4-alpha-hydroxytetrahydrobiopterin dehydratase activity2.55E-04
32GO:0015088: copper uptake transmembrane transporter activity2.55E-04
33GO:0004830: tryptophan-tRNA ligase activity2.55E-04
34GO:0010347: L-galactose-1-phosphate phosphatase activity2.55E-04
35GO:0042286: glutamate-1-semialdehyde 2,1-aminomutase activity2.55E-04
36GO:0051082: unfolded protein binding4.45E-04
37GO:0102083: 7,8-dihydromonapterin aldolase activity5.64E-04
38GO:0052832: inositol monophosphate 3-phosphatase activity5.64E-04
39GO:0000774: adenyl-nucleotide exchange factor activity5.64E-04
40GO:0008934: inositol monophosphate 1-phosphatase activity5.64E-04
41GO:0016630: protochlorophyllide reductase activity5.64E-04
42GO:0052833: inositol monophosphate 4-phosphatase activity5.64E-04
43GO:0019171: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity5.64E-04
44GO:0004150: dihydroneopterin aldolase activity5.64E-04
45GO:0004066: asparagine synthase (glutamine-hydrolyzing) activity5.64E-04
46GO:0004148: dihydrolipoyl dehydrogenase activity9.15E-04
47GO:0004751: ribose-5-phosphate isomerase activity9.15E-04
48GO:0070402: NADPH binding9.15E-04
49GO:0005528: FK506 binding1.14E-03
50GO:0051087: chaperone binding1.25E-03
51GO:0004742: dihydrolipoyllysine-residue acetyltransferase activity1.31E-03
52GO:0035529: NADH pyrophosphatase activity1.31E-03
53GO:0048487: beta-tubulin binding1.31E-03
54GO:0016149: translation release factor activity, codon specific1.31E-03
55GO:0003865: 3-oxo-5-alpha-steroid 4-dehydrogenase activity1.31E-03
56GO:0004550: nucleoside diphosphate kinase activity1.31E-03
57GO:0043023: ribosomal large subunit binding1.31E-03
58GO:0008097: 5S rRNA binding1.31E-03
59GO:0022891: substrate-specific transmembrane transporter activity1.63E-03
60GO:0004045: aminoacyl-tRNA hydrolase activity1.75E-03
61GO:0016987: sigma factor activity1.75E-03
62GO:0043495: protein anchor1.75E-03
63GO:0004659: prenyltransferase activity1.75E-03
64GO:0001053: plastid sigma factor activity1.75E-03
65GO:0004845: uracil phosphoribosyltransferase activity1.75E-03
66GO:0009922: fatty acid elongase activity2.23E-03
67GO:0003959: NADPH dehydrogenase activity2.23E-03
68GO:0030414: peptidase inhibitor activity2.23E-03
69GO:0004623: phospholipase A2 activity2.23E-03
70GO:0004040: amidase activity2.23E-03
71GO:0003989: acetyl-CoA carboxylase activity2.23E-03
72GO:0031177: phosphopantetheine binding2.75E-03
73GO:0016462: pyrophosphatase activity2.75E-03
74GO:0015271: outward rectifier potassium channel activity2.75E-03
75GO:0004605: phosphatidate cytidylyltransferase activity2.75E-03
76GO:0008441: 3'(2'),5'-bisphosphate nucleotidase activity3.30E-03
77GO:0004849: uridine kinase activity3.30E-03
78GO:0000035: acyl binding3.30E-03
79GO:0004124: cysteine synthase activity3.30E-03
80GO:0042803: protein homodimerization activity3.88E-03
81GO:0019899: enzyme binding3.89E-03
82GO:0016168: chlorophyll binding4.20E-03
83GO:0000036: ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process4.52E-03
84GO:0004033: aldo-keto reductase (NADP) activity4.52E-03
85GO:0005267: potassium channel activity5.18E-03
86GO:0016627: oxidoreductase activity, acting on the CH-CH group of donors5.86E-03
87GO:0003747: translation release factor activity5.86E-03
88GO:0005381: iron ion transmembrane transporter activity6.58E-03
89GO:0008047: enzyme activator activity7.33E-03
90GO:0004864: protein phosphatase inhibitor activity7.33E-03
91GO:0042802: identical protein binding7.45E-03
92GO:0046961: proton-transporting ATPase activity, rotational mechanism8.11E-03
93GO:0044183: protein binding involved in protein folding8.11E-03
94GO:0016887: ATPase activity9.66E-03
95GO:0031072: heat shock protein binding9.75E-03
96GO:0005216: ion channel activity1.43E-02
97GO:0003723: RNA binding1.49E-02
98GO:0004176: ATP-dependent peptidase activity1.53E-02
99GO:0015035: protein disulfide oxidoreductase activity1.68E-02
100GO:0016491: oxidoreductase activity1.73E-02
101GO:0003727: single-stranded RNA binding1.85E-02
102GO:0047134: protein-disulfide reductase activity1.95E-02
103GO:0004812: aminoacyl-tRNA ligase activity1.95E-02
104GO:0003729: mRNA binding2.13E-02
105GO:0030170: pyridoxal phosphate binding2.27E-02
106GO:0004791: thioredoxin-disulfide reductase activity2.29E-02
107GO:0016671: oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor2.78E-02
108GO:0005509: calcium ion binding3.01E-02
109GO:0008483: transaminase activity3.03E-02
110GO:0016722: oxidoreductase activity, oxidizing metal ions3.03E-02
111GO:0008237: metallopeptidase activity3.03E-02
112GO:0005200: structural constituent of cytoskeleton3.03E-02
113GO:0008236: serine-type peptidase activity3.83E-02
114GO:0015450: P-P-bond-hydrolysis-driven protein transmembrane transporter activity3.97E-02
115GO:0005096: GTPase activator activity4.12E-02
116GO:0008168: methyltransferase activity4.20E-02
117GO:0004222: metalloendopeptidase activity4.26E-02
118GO:0004601: peroxidase activity4.36E-02
119GO:0003746: translation elongation factor activity4.70E-02
RankGO TermAdjusted P value
1GO:0009507: chloroplast8.65E-66
2GO:0009570: chloroplast stroma2.03E-54
3GO:0009941: chloroplast envelope3.28E-37
4GO:0009535: chloroplast thylakoid membrane1.94E-23
5GO:0009579: thylakoid1.23E-22
6GO:0005840: ribosome1.77E-10
7GO:0031977: thylakoid lumen3.92E-10
8GO:0009543: chloroplast thylakoid lumen8.92E-10
9GO:0009534: chloroplast thylakoid8.72E-09
10GO:0009654: photosystem II oxygen evolving complex2.99E-06
11GO:0009536: plastid3.34E-06
12GO:0030956: glutamyl-tRNA(Gln) amidotransferase complex2.55E-04
13GO:0009515: granal stacked thylakoid2.55E-04
14GO:0009923: fatty acid elongase complex2.55E-04
15GO:0019898: extrinsic component of membrane2.61E-04
16GO:0031969: chloroplast membrane5.80E-04
17GO:0009707: chloroplast outer membrane6.53E-04
18GO:0009528: plastid inner membrane9.15E-04
19GO:0010007: magnesium chelatase complex9.15E-04
20GO:0009509: chromoplast9.15E-04
21GO:0009317: acetyl-CoA carboxylase complex9.15E-04
22GO:0042651: thylakoid membrane1.25E-03
23GO:0009532: plastid stroma1.37E-03
24GO:0009526: plastid envelope1.75E-03
25GO:0031897: Tic complex1.75E-03
26GO:0009527: plastid outer membrane1.75E-03
27GO:0048046: apoplast2.18E-03
28GO:0000220: vacuolar proton-transporting V-type ATPase, V0 domain2.23E-03
29GO:0055035: plastid thylakoid membrane2.23E-03
30GO:0009523: photosystem II2.57E-03
31GO:0009706: chloroplast inner membrane2.74E-03
32GO:0010319: stromule3.54E-03
33GO:0030529: intracellular ribonucleoprotein complex3.97E-03
34GO:0009539: photosystem II reaction center5.18E-03
35GO:0045298: tubulin complex5.86E-03
36GO:0005763: mitochondrial small ribosomal subunit5.86E-03
37GO:0032040: small-subunit processome8.92E-03
38GO:0009508: plastid chromosome9.75E-03
39GO:0022626: cytosolic ribosome1.11E-02
40GO:0015935: small ribosomal subunit1.53E-02
41GO:0031410: cytoplasmic vesicle1.64E-02
42GO:0005759: mitochondrial matrix2.57E-02
43GO:0009295: nucleoid3.03E-02
44GO:0005778: peroxisomal membrane3.03E-02
45GO:0046658: anchored component of plasma membrane3.74E-02
46GO:0015934: large ribosomal subunit4.41E-02
47GO:0005618: cell wall4.52E-02
48GO:0009505: plant-type cell wall4.68E-02
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Gene type



Gene DE type