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

AT3G56040

GO-BP
GO-MF
GO-CC
RankGO TermAdjusted P value
1GO:0006428: isoleucyl-tRNA aminoacylation0.00E+00
2GO:0090042: tubulin deacetylation0.00E+00
3GO:0006399: tRNA metabolic process0.00E+00
4GO:0002184: cytoplasmic translational termination0.00E+00
5GO:0006780: uroporphyrinogen III biosynthetic process0.00E+00
6GO:0070681: glutaminyl-tRNAGln biosynthesis via transamidation0.00E+00
7GO:0016553: base conversion or substitution editing0.00E+00
8GO:2000121: regulation of removal of superoxide radicals0.00E+00
9GO:0061635: regulation of protein complex stability0.00E+00
10GO:0009773: photosynthetic electron transport in photosystem I1.38E-07
11GO:0015995: chlorophyll biosynthetic process1.62E-07
12GO:0032544: plastid translation1.31E-06
13GO:0010206: photosystem II repair2.07E-06
14GO:0010275: NAD(P)H dehydrogenase complex assembly1.47E-05
15GO:0015979: photosynthesis1.93E-05
16GO:2001141: regulation of RNA biosynthetic process1.03E-04
17GO:0080170: hydrogen peroxide transmembrane transport1.03E-04
18GO:0015994: chlorophyll metabolic process1.77E-04
19GO:0006546: glycine catabolic process1.77E-04
20GO:0009735: response to cytokinin2.29E-04
21GO:0006810: transport2.72E-04
22GO:0006412: translation2.78E-04
23GO:0042549: photosystem II stabilization3.77E-04
24GO:0043489: RNA stabilization5.80E-04
25GO:0043266: regulation of potassium ion transport5.80E-04
26GO:0071370: cellular response to gibberellin stimulus5.80E-04
27GO:0010480: microsporocyte differentiation5.80E-04
28GO:0031338: regulation of vesicle fusion5.80E-04
29GO:0000481: maturation of 5S rRNA5.80E-04
30GO:0042547: cell wall modification involved in multidimensional cell growth5.80E-04
31GO:0071461: cellular response to redox state5.80E-04
32GO:2000021: regulation of ion homeostasis5.80E-04
33GO:0010028: xanthophyll cycle5.80E-04
34GO:0034337: RNA folding5.80E-04
35GO:0010729: positive regulation of hydrogen peroxide biosynthetic process5.80E-04
36GO:0000476: maturation of 4.5S rRNA5.80E-04
37GO:0000967: rRNA 5'-end processing5.80E-04
38GO:0071482: cellular response to light stimulus9.71E-04
39GO:0010541: acropetal auxin transport1.25E-03
40GO:0034755: iron ion transmembrane transport1.25E-03
41GO:0016122: xanthophyll metabolic process1.25E-03
42GO:0030388: fructose 1,6-bisphosphate metabolic process1.25E-03
43GO:0010270: photosystem II oxygen evolving complex assembly1.25E-03
44GO:0034470: ncRNA processing1.25E-03
45GO:0080005: photosystem stoichiometry adjustment1.25E-03
46GO:1900871: chloroplast mRNA modification1.25E-03
47GO:0006352: DNA-templated transcription, initiation1.85E-03
48GO:0019684: photosynthesis, light reaction1.85E-03
49GO:0006518: peptide metabolic process2.05E-03
50GO:0006013: mannose metabolic process2.05E-03
51GO:0043617: cellular response to sucrose starvation2.05E-03
52GO:0010160: formation of animal organ boundary2.05E-03
53GO:0045493: xylan catabolic process2.05E-03
54GO:0090630: activation of GTPase activity2.05E-03
55GO:2001295: malonyl-CoA biosynthetic process2.05E-03
56GO:0006000: fructose metabolic process2.05E-03
57GO:0010027: thylakoid membrane organization2.16E-03
58GO:0006094: gluconeogenesis2.41E-03
59GO:0009767: photosynthetic electron transport chain2.41E-03
60GO:1901332: negative regulation of lateral root development2.98E-03
61GO:0016556: mRNA modification2.98E-03
62GO:0010258: NADH dehydrogenase complex (plastoquinone) assembly2.98E-03
63GO:0051513: regulation of monopolar cell growth2.98E-03
64GO:0009152: purine ribonucleotide biosynthetic process2.98E-03
65GO:0046653: tetrahydrofolate metabolic process2.98E-03
66GO:0034059: response to anoxia2.98E-03
67GO:0043481: anthocyanin accumulation in tissues in response to UV light2.98E-03
68GO:0006424: glutamyl-tRNA aminoacylation2.98E-03
69GO:0043433: negative regulation of sequence-specific DNA binding transcription factor activity2.98E-03
70GO:0005985: sucrose metabolic process3.06E-03
71GO:0010218: response to far red light3.45E-03
72GO:0009658: chloroplast organization3.46E-03
73GO:0042254: ribosome biogenesis3.58E-03
74GO:0008152: metabolic process3.63E-03
75GO:0010037: response to carbon dioxide4.02E-03
76GO:0015976: carbon utilization4.02E-03
77GO:0019464: glycine decarboxylation via glycine cleavage system4.02E-03
78GO:0045727: positive regulation of translation4.02E-03
79GO:2000122: negative regulation of stomatal complex development4.02E-03
80GO:0030104: water homeostasis4.02E-03
81GO:0009637: response to blue light4.12E-03
82GO:0061077: chaperone-mediated protein folding4.60E-03
83GO:0009814: defense response, incompatible interaction5.04E-03
84GO:0032543: mitochondrial translation5.16E-03
85GO:0009107: lipoate biosynthetic process5.16E-03
86GO:0006465: signal peptide processing5.16E-03
87GO:0000304: response to singlet oxygen5.16E-03
88GO:0009247: glycolipid biosynthetic process5.16E-03
89GO:0034052: positive regulation of plant-type hypersensitive response5.16E-03
90GO:0010114: response to red light5.71E-03
91GO:0006633: fatty acid biosynthetic process5.75E-03
92GO:0006828: manganese ion transport6.40E-03
93GO:0032973: amino acid export6.40E-03
94GO:0000741: karyogamy6.40E-03
95GO:0006751: glutathione catabolic process6.40E-03
96GO:0000470: maturation of LSU-rRNA6.40E-03
97GO:0006655: phosphatidylglycerol biosynthetic process6.40E-03
98GO:0060918: auxin transport6.40E-03
99GO:1902456: regulation of stomatal opening6.40E-03
100GO:0010190: cytochrome b6f complex assembly6.40E-03
101GO:0006086: acetyl-CoA biosynthetic process from pyruvate6.40E-03
102GO:0034220: ion transmembrane transport7.03E-03
103GO:0000413: protein peptidyl-prolyl isomerization7.03E-03
104GO:0009958: positive gravitropism7.59E-03
105GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)7.73E-03
106GO:0006458: 'de novo' protein folding7.73E-03
107GO:0042026: protein refolding7.73E-03
108GO:0051603: proteolysis involved in cellular protein catabolic process8.74E-03
109GO:0009395: phospholipid catabolic process9.15E-03
110GO:0009772: photosynthetic electron transport in photosystem II9.15E-03
111GO:0043090: amino acid import9.15E-03
112GO:1900056: negative regulation of leaf senescence9.15E-03
113GO:0048437: floral organ development9.15E-03
114GO:0010196: nonphotochemical quenching9.15E-03
115GO:0043068: positive regulation of programmed cell death1.07E-02
116GO:0019375: galactolipid biosynthetic process1.07E-02
117GO:0032508: DNA duplex unwinding1.07E-02
118GO:0010492: maintenance of shoot apical meristem identity1.07E-02
119GO:0006526: arginine biosynthetic process1.23E-02
120GO:0006002: fructose 6-phosphate metabolic process1.23E-02
121GO:0048507: meristem development1.39E-02
122GO:0000373: Group II intron splicing1.39E-02
123GO:0005975: carbohydrate metabolic process1.39E-02
124GO:0009051: pentose-phosphate shunt, oxidative branch1.39E-02
125GO:0090305: nucleic acid phosphodiester bond hydrolysis1.39E-02
126GO:0006098: pentose-phosphate shunt1.39E-02
127GO:0080144: amino acid homeostasis1.39E-02
128GO:0006508: proteolysis1.47E-02
129GO:0042128: nitrate assimilation1.53E-02
130GO:0010205: photoinhibition1.57E-02
131GO:0009638: phototropism1.57E-02
132GO:0006779: porphyrin-containing compound biosynthetic process1.57E-02
133GO:1900865: chloroplast RNA modification1.57E-02
134GO:0006782: protoporphyrinogen IX biosynthetic process1.75E-02
135GO:0043069: negative regulation of programmed cell death1.75E-02
136GO:0018298: protein-chromophore linkage1.79E-02
137GO:0009817: defense response to fungus, incompatible interaction1.79E-02
138GO:0006879: cellular iron ion homeostasis1.94E-02
139GO:0018119: peptidyl-cysteine S-nitrosylation1.94E-02
140GO:0048229: gametophyte development1.94E-02
141GO:0006816: calcium ion transport1.94E-02
142GO:0009089: lysine biosynthetic process via diaminopimelate1.94E-02
143GO:0009407: toxin catabolic process1.97E-02
144GO:0009790: embryo development2.13E-02
145GO:0016024: CDP-diacylglycerol biosynthetic process2.14E-02
146GO:0008361: regulation of cell size2.14E-02
147GO:0045454: cell redox homeostasis2.33E-02
148GO:0006006: glucose metabolic process2.34E-02
149GO:0009718: anthocyanin-containing compound biosynthetic process2.34E-02
150GO:0010075: regulation of meristem growth2.34E-02
151GO:0005986: sucrose biosynthetic process2.34E-02
152GO:0030048: actin filament-based movement2.34E-02
153GO:0019253: reductive pentose-phosphate cycle2.56E-02
154GO:0010540: basipetal auxin transport2.56E-02
155GO:0009934: regulation of meristem structural organization2.56E-02
156GO:0010207: photosystem II assembly2.56E-02
157GO:0055114: oxidation-reduction process2.59E-02
158GO:0009409: response to cold2.62E-02
159GO:0009451: RNA modification2.70E-02
160GO:0006631: fatty acid metabolic process2.70E-02
161GO:0010030: positive regulation of seed germination2.77E-02
162GO:0006636: unsaturated fatty acid biosynthetic process3.00E-02
163GO:0006833: water transport3.00E-02
164GO:0000027: ribosomal large subunit assembly3.23E-02
165GO:0007010: cytoskeleton organization3.23E-02
166GO:0009636: response to toxic substance3.29E-02
167GO:0009768: photosynthesis, light harvesting in photosystem I3.46E-02
168GO:0016575: histone deacetylation3.46E-02
169GO:0006418: tRNA aminoacylation for protein translation3.46E-02
170GO:0042742: defense response to bacterium3.53E-02
171GO:0009664: plant-type cell wall organization3.67E-02
172GO:0048511: rhythmic process3.70E-02
173GO:0031408: oxylipin biosynthetic process3.70E-02
174GO:0006364: rRNA processing3.94E-02
175GO:0010017: red or far-red light signaling pathway3.95E-02
176GO:0006012: galactose metabolic process4.20E-02
177GO:0009831: plant-type cell wall modification involved in multidimensional cell growth4.20E-02
178GO:0009306: protein secretion4.46E-02
179GO:0048443: stamen development4.46E-02
180GO:0006096: glycolytic process4.65E-02
181GO:0009789: positive regulation of abscisic acid-activated signaling pathway4.72E-02
182GO:0080022: primary root development4.98E-02
183GO:0048653: anther development4.98E-02
184GO:0042631: cellular response to water deprivation4.98E-02
RankGO TermAdjusted P value
1GO:0051721: protein phosphatase 2A binding0.00E+00
2GO:0043014: alpha-tubulin binding0.00E+00
3GO:0047538: 2-carboxy-D-arabinitol-1-phosphatase activity0.00E+00
4GO:0080176: xyloglucan 1,6-alpha-xylosidase activity0.00E+00
5GO:0042903: tubulin deacetylase activity0.00E+00
6GO:0004822: isoleucine-tRNA ligase activity0.00E+00
7GO:0004852: uroporphyrinogen-III synthase activity0.00E+00
8GO:0008942: nitrite reductase [NAD(P)H] activity0.00E+00
9GO:0046406: magnesium protoporphyrin IX methyltransferase activity0.00E+00
10GO:0047513: 1,2-alpha-L-fucosidase activity0.00E+00
11GO:0061634: alpha-D-xyloside xylohydrolase0.00E+00
12GO:0046422: violaxanthin de-epoxidase activity0.00E+00
13GO:0019843: rRNA binding9.93E-14
14GO:0003755: peptidyl-prolyl cis-trans isomerase activity7.72E-09
15GO:0005528: FK506 binding2.88E-08
16GO:0016851: magnesium chelatase activity8.81E-07
17GO:0003735: structural constituent of ribosome6.00E-06
18GO:0051920: peroxiredoxin activity1.75E-05
19GO:0016209: antioxidant activity4.00E-05
20GO:0001053: plastid sigma factor activity1.77E-04
21GO:0016987: sigma factor activity1.77E-04
22GO:0008266: poly(U) RNA binding2.73E-04
23GO:0045156: electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity5.01E-04
24GO:0003867: 4-aminobutyrate transaminase activity5.80E-04
25GO:0045485: omega-6 fatty acid desaturase activity5.80E-04
26GO:0003942: N-acetyl-gamma-glutamyl-phosphate reductase activity5.80E-04
27GO:0050567: glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity5.80E-04
28GO:0004856: xylulokinase activity5.80E-04
29GO:0080132: fatty acid alpha-hydroxylase activity5.80E-04
30GO:0004033: aldo-keto reductase (NADP) activity7.99E-04
31GO:0008839: 4-hydroxy-tetrahydrodipicolinate reductase1.25E-03
32GO:0017118: lipoyltransferase activity1.25E-03
33GO:0047746: chlorophyllase activity1.25E-03
34GO:0016868: intramolecular transferase activity, phosphotransferases1.25E-03
35GO:0003839: gamma-glutamylcyclotransferase activity1.25E-03
36GO:0016415: octanoyltransferase activity1.25E-03
37GO:0004047: aminomethyltransferase activity1.25E-03
38GO:0046509: 1,2-diacylglycerol 3-beta-galactosyltransferase activity1.25E-03
39GO:0042132: fructose 1,6-bisphosphate 1-phosphatase activity1.25E-03
40GO:0002161: aminoacyl-tRNA editing activity2.05E-03
41GO:0004075: biotin carboxylase activity2.05E-03
42GO:0030267: glyoxylate reductase (NADP) activity2.05E-03
43GO:0016742: hydroxymethyl-, formyl- and related transferase activity2.05E-03
44GO:0008864: formyltetrahydrofolate deformylase activity2.05E-03
45GO:0016620: oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor2.05E-03
46GO:0003863: 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity2.05E-03
47GO:0016787: hydrolase activity2.32E-03
48GO:0008236: serine-type peptidase activity2.85E-03
49GO:0048487: beta-tubulin binding2.98E-03
50GO:0043023: ribosomal large subunit binding2.98E-03
51GO:0008508: bile acid:sodium symporter activity2.98E-03
52GO:0001872: (1->3)-beta-D-glucan binding2.98E-03
53GO:0004375: glycine dehydrogenase (decarboxylating) activity2.98E-03
54GO:0019201: nucleotide kinase activity2.98E-03
55GO:0035250: UDP-galactosyltransferase activity2.98E-03
56GO:0005096: GTPase activator activity3.24E-03
57GO:0004222: metalloendopeptidase activity3.45E-03
58GO:0016491: oxidoreductase activity3.92E-03
59GO:0046556: alpha-L-arabinofuranosidase activity4.02E-03
60GO:0004345: glucose-6-phosphate dehydrogenase activity4.02E-03
61GO:0016655: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor4.02E-03
62GO:0008574: ATP-dependent microtubule motor activity, plus-end-directed4.02E-03
63GO:0004739: pyruvate dehydrogenase (acetyl-transferring) activity4.02E-03
64GO:0009044: xylan 1,4-beta-xylosidase activity4.02E-03
65GO:0004252: serine-type endopeptidase activity4.75E-03
66GO:0016773: phosphotransferase activity, alcohol group as acceptor5.16E-03
67GO:0017137: Rab GTPase binding5.16E-03
68GO:0003989: acetyl-CoA carboxylase activity5.16E-03
69GO:0030570: pectate lyase activity5.51E-03
70GO:0004185: serine-type carboxypeptidase activity5.71E-03
71GO:0051537: 2 iron, 2 sulfur cluster binding6.31E-03
72GO:0004130: cytochrome-c peroxidase activity6.40E-03
73GO:0004366: glycerol-3-phosphate O-acyltransferase activity6.40E-03
74GO:0042578: phosphoric ester hydrolase activity6.40E-03
75GO:0008200: ion channel inhibitor activity6.40E-03
76GO:0004332: fructose-bisphosphate aldolase activity6.40E-03
77GO:0004723: calcium-dependent protein serine/threonine phosphatase activity7.73E-03
78GO:0004559: alpha-mannosidase activity7.73E-03
79GO:0004017: adenylate kinase activity7.73E-03
80GO:0015631: tubulin binding7.73E-03
81GO:0004616: phosphogluconate dehydrogenase (decarboxylating) activity7.73E-03
82GO:0043022: ribosome binding1.07E-02
83GO:0004564: beta-fructofuranosidase activity1.07E-02
84GO:0004034: aldose 1-epimerase activity1.07E-02
85GO:0005509: calcium ion binding1.18E-02
86GO:0032041: NAD-dependent histone deacetylase activity (H3-K14 specific)1.23E-02
87GO:0004601: peroxidase activity1.29E-02
88GO:0015250: water channel activity1.37E-02
89GO:0016168: chlorophyll binding1.45E-02
90GO:0005384: manganese ion transmembrane transporter activity1.57E-02
91GO:0004575: sucrose alpha-glucosidase activity1.57E-02
92GO:0005381: iron ion transmembrane transporter activity1.57E-02
93GO:0004553: hydrolase activity, hydrolyzing O-glycosyl compounds1.58E-02
94GO:0016829: lyase activity1.93E-02
95GO:0044183: protein binding involved in protein folding1.94E-02
96GO:0047372: acylglycerol lipase activity1.94E-02
97GO:0000049: tRNA binding2.14E-02
98GO:0008378: galactosyltransferase activity2.14E-02
99GO:0004022: alcohol dehydrogenase (NAD) activity2.34E-02
100GO:0010329: auxin efflux transmembrane transporter activity2.34E-02
101GO:0004089: carbonate dehydratase activity2.34E-02
102GO:0015095: magnesium ion transmembrane transporter activity2.34E-02
103GO:0031072: heat shock protein binding2.34E-02
104GO:0004565: beta-galactosidase activity2.34E-02
105GO:0003993: acid phosphatase activity2.37E-02
106GO:0042973: glucan endo-1,3-beta-D-glucosidase activity2.56E-02
107GO:0003774: motor activity2.56E-02
108GO:0004364: glutathione transferase activity2.81E-02
109GO:0031409: pigment binding3.00E-02
110GO:0004407: histone deacetylase activity3.23E-02
111GO:0043424: protein histidine kinase binding3.46E-02
112GO:0015079: potassium ion transmembrane transporter activity3.46E-02
113GO:0004519: endonuclease activity3.59E-02
114GO:0004176: ATP-dependent peptidase activity3.70E-02
115GO:0033612: receptor serine/threonine kinase binding3.70E-02
116GO:0003899: DNA-directed 5'-3' RNA polymerase activity3.94E-02
117GO:0022891: substrate-specific transmembrane transporter activity4.20E-02
118GO:0003756: protein disulfide isomerase activity4.46E-02
119GO:0016788: hydrolase activity, acting on ester bonds4.61E-02
120GO:0004812: aminoacyl-tRNA ligase activity4.72E-02
RankGO TermAdjusted P value
1GO:0005943: phosphatidylinositol 3-kinase complex, class IA0.00E+00
2GO:0009344: nitrite reductase complex [NAD(P)H]0.00E+00
3GO:0098572: stromal side of plastid thylakoid membrane0.00E+00
4GO:0009507: chloroplast8.10E-58
5GO:0009534: chloroplast thylakoid4.33E-37
6GO:0009570: chloroplast stroma7.38E-33
7GO:0009535: chloroplast thylakoid membrane5.80E-31
8GO:0009941: chloroplast envelope8.27E-29
9GO:0009543: chloroplast thylakoid lumen4.11E-24
10GO:0009579: thylakoid1.55E-14
11GO:0031977: thylakoid lumen1.14E-13
12GO:0010598: NAD(P)H dehydrogenase complex (plastoquinone)3.29E-10
13GO:0010007: magnesium chelatase complex1.85E-07
14GO:0009654: photosystem II oxygen evolving complex1.53E-06
15GO:0019898: extrinsic component of membrane1.11E-05
16GO:0030095: chloroplast photosystem II1.53E-05
17GO:0005840: ribosome1.81E-05
18GO:0009533: chloroplast stromal thylakoid2.73E-05
19GO:0000311: plastid large ribosomal subunit1.91E-04
20GO:0009547: plastid ribosome5.80E-04
21GO:0043674: columella5.80E-04
22GO:0030956: glutamyl-tRNA(Gln) amidotransferase complex5.80E-04
23GO:0009706: chloroplast inner membrane6.07E-04
24GO:0009505: plant-type cell wall1.29E-03
25GO:0048046: apoplast2.12E-03
26GO:0009508: plastid chromosome2.41E-03
27GO:0000312: plastid small ribosomal subunit2.73E-03
28GO:0009531: secondary cell wall2.98E-03
29GO:0005775: vacuolar lumen2.98E-03
30GO:0005960: glycine cleavage complex2.98E-03
31GO:0009536: plastid3.26E-03
32GO:0016020: membrane3.28E-03
33GO:0010287: plastoglobule3.73E-03
34GO:0009523: photosystem II8.77E-03
35GO:0042807: central vacuole9.15E-03
36GO:0046658: anchored component of plasma membrane1.02E-02
37GO:0009295: nucleoid1.21E-02
38GO:0010319: stromule1.21E-02
39GO:0005618: cell wall1.35E-02
40GO:0042644: chloroplast nucleoid1.39E-02
41GO:0016459: myosin complex1.75E-02
42GO:0031969: chloroplast membrane1.78E-02
43GO:0015934: large ribosomal subunit2.07E-02
44GO:0032040: small-subunit processome2.14E-02
45GO:0030076: light-harvesting complex2.77E-02
46GO:0043234: protein complex3.00E-02
47GO:0042651: thylakoid membrane3.46E-02
48GO:0005871: kinesin complex4.72E-02
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Gene type



Gene DE type