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

AT3G04940

GO-BP
GO-MF
GO-CC
RankGO TermAdjusted P value
1GO:0005996: monosaccharide metabolic process0.00E+00
2GO:0070272: proton-transporting ATP synthase complex biogenesis0.00E+00
3GO:0090042: tubulin deacetylation0.00E+00
4GO:0042820: vitamin B6 catabolic process0.00E+00
5GO:0006399: tRNA metabolic process0.00E+00
6GO:0070125: mitochondrial translational elongation0.00E+00
7GO:0070681: glutaminyl-tRNAGln biosynthesis via transamidation0.00E+00
8GO:0006223: uracil salvage0.00E+00
9GO:0006428: isoleucyl-tRNA aminoacylation0.00E+00
10GO:0006642: triglyceride mobilization0.00E+00
11GO:0016553: base conversion or substitution editing0.00E+00
12GO:0042821: pyridoxal biosynthetic process0.00E+00
13GO:0009658: chloroplast organization2.52E-11
14GO:0015979: photosynthesis5.72E-07
15GO:0009773: photosynthetic electron transport in photosystem I9.47E-07
16GO:0019253: reductive pentose-phosphate cycle2.38E-06
17GO:0010275: NAD(P)H dehydrogenase complex assembly4.77E-06
18GO:1902326: positive regulation of chlorophyll biosynthetic process4.77E-06
19GO:0006096: glycolytic process6.20E-06
20GO:0009657: plastid organization1.38E-05
21GO:0071482: cellular response to light stimulus1.38E-05
22GO:2001141: regulation of RNA biosynthetic process3.75E-05
23GO:0010258: NADH dehydrogenase complex (plastoquinone) assembly3.75E-05
24GO:0006352: DNA-templated transcription, initiation4.25E-05
25GO:0006094: gluconeogenesis6.51E-05
26GO:0009767: photosynthetic electron transport chain6.51E-05
27GO:0006546: glycine catabolic process6.70E-05
28GO:0010020: chloroplast fission7.88E-05
29GO:0006810: transport1.50E-04
30GO:0006086: acetyl-CoA biosynthetic process from pyruvate1.52E-04
31GO:0042549: photosystem II stabilization1.52E-04
32GO:0010190: cytochrome b6f complex assembly1.52E-04
33GO:0046686: response to cadmium ion1.82E-04
34GO:0042026: protein refolding2.07E-04
35GO:0010196: nonphotochemical quenching2.70E-04
36GO:0016117: carotenoid biosynthetic process2.78E-04
37GO:0042335: cuticle development3.09E-04
38GO:0043489: RNA stabilization3.24E-04
39GO:1904966: positive regulation of vitamin E biosynthetic process3.24E-04
40GO:0046166: glyceraldehyde-3-phosphate biosynthetic process3.24E-04
41GO:0006723: cuticle hydrocarbon biosynthetic process3.24E-04
42GO:1904964: positive regulation of phytol biosynthetic process3.24E-04
43GO:0009443: pyridoxal 5'-phosphate salvage3.24E-04
44GO:0032544: plastid translation4.17E-04
45GO:0009662: etioplast organization7.07E-04
46GO:1904143: positive regulation of carotenoid biosynthetic process7.07E-04
47GO:0080183: response to photooxidative stress7.07E-04
48GO:0030388: fructose 1,6-bisphosphate metabolic process7.07E-04
49GO:0006415: translational termination7.96E-04
50GO:0018119: peptidyl-cysteine S-nitrosylation7.96E-04
51GO:0009073: aromatic amino acid family biosynthetic process7.96E-04
52GO:0018298: protein-chromophore linkage1.01E-03
53GO:0006518: peptide metabolic process1.15E-03
54GO:0006696: ergosterol biosynthetic process1.15E-03
55GO:0030865: cortical cytoskeleton organization1.15E-03
56GO:0032504: multicellular organism reproduction1.15E-03
57GO:0000913: preprophase band assembly1.15E-03
58GO:0006000: fructose metabolic process1.15E-03
59GO:0043447: alkane biosynthetic process1.15E-03
60GO:0019563: glycerol catabolic process1.15E-03
61GO:0010207: photosystem II assembly1.16E-03
62GO:0090351: seedling development1.29E-03
63GO:0010731: protein glutathionylation1.65E-03
64GO:0006424: glutamyl-tRNA aminoacylation1.65E-03
65GO:0016556: mRNA modification1.65E-03
66GO:0043572: plastid fission1.65E-03
67GO:0051085: chaperone mediated protein folding requiring cofactor1.65E-03
68GO:0009768: photosynthesis, light harvesting in photosystem I1.76E-03
69GO:0061077: chaperone-mediated protein folding1.93E-03
70GO:0031408: oxylipin biosynthetic process1.93E-03
71GO:0080092: regulation of pollen tube growth2.11E-03
72GO:0044206: UMP salvage2.21E-03
73GO:0071483: cellular response to blue light2.21E-03
74GO:0010037: response to carbon dioxide2.21E-03
75GO:0015976: carbon utilization2.21E-03
76GO:0051781: positive regulation of cell division2.21E-03
77GO:0019464: glycine decarboxylation via glycine cleavage system2.21E-03
78GO:0006085: acetyl-CoA biosynthetic process2.21E-03
79GO:0045727: positive regulation of translation2.21E-03
80GO:2000122: negative regulation of stomatal complex development2.21E-03
81GO:0032543: mitochondrial translation2.82E-03
82GO:0006564: L-serine biosynthetic process2.82E-03
83GO:0043097: pyrimidine nucleoside salvage2.82E-03
84GO:0010236: plastoquinone biosynthetic process2.82E-03
85GO:0006461: protein complex assembly2.82E-03
86GO:1902183: regulation of shoot apical meristem development2.82E-03
87GO:0000304: response to singlet oxygen2.82E-03
88GO:0006206: pyrimidine nucleobase metabolic process3.49E-03
89GO:0000470: maturation of LSU-rRNA3.49E-03
90GO:0009409: response to cold4.00E-03
91GO:0032502: developmental process4.16E-03
92GO:0006458: 'de novo' protein folding4.20E-03
93GO:1901259: chloroplast rRNA processing4.20E-03
94GO:0030488: tRNA methylation4.20E-03
95GO:0009854: oxidative photosynthetic carbon pathway4.20E-03
96GO:0055114: oxidation-reduction process4.25E-03
97GO:0009645: response to low light intensity stimulus4.95E-03
98GO:0006400: tRNA modification4.95E-03
99GO:0010027: thylakoid membrane organization5.63E-03
100GO:0048564: photosystem I assembly5.76E-03
101GO:0008610: lipid biosynthetic process5.76E-03
102GO:0017004: cytochrome complex assembly6.60E-03
103GO:0006002: fructose 6-phosphate metabolic process6.60E-03
104GO:0006075: (1->3)-beta-D-glucan biosynthetic process6.60E-03
105GO:0015995: chlorophyll biosynthetic process6.63E-03
106GO:2000024: regulation of leaf development7.48E-03
107GO:0000902: cell morphogenesis7.48E-03
108GO:0006098: pentose-phosphate shunt7.48E-03
109GO:1900865: chloroplast RNA modification8.41E-03
110GO:0006629: lipid metabolic process8.48E-03
111GO:0006457: protein folding9.14E-03
112GO:0009637: response to blue light9.33E-03
113GO:0009853: photorespiration9.33E-03
114GO:0048829: root cap development9.37E-03
115GO:0045036: protein targeting to chloroplast9.37E-03
116GO:0008152: metabolic process9.83E-03
117GO:0000272: polysaccharide catabolic process1.04E-02
118GO:0019684: photosynthesis, light reaction1.04E-02
119GO:0006631: fatty acid metabolic process1.11E-02
120GO:0045037: protein import into chloroplast stroma1.14E-02
121GO:0010114: response to red light1.21E-02
122GO:0006006: glucose metabolic process1.25E-02
123GO:0005986: sucrose biosynthetic process1.25E-02
124GO:0010143: cutin biosynthetic process1.36E-02
125GO:0009636: response to toxic substance1.36E-02
126GO:0006855: drug transmembrane transport1.41E-02
127GO:0010025: wax biosynthetic process1.60E-02
128GO:0009116: nucleoside metabolic process1.72E-02
129GO:0009944: polarity specification of adaxial/abaxial axis1.72E-02
130GO:0009695: jasmonic acid biosynthetic process1.84E-02
131GO:0007017: microtubule-based process1.84E-02
132GO:0016575: histone deacetylation1.84E-02
133GO:0006418: tRNA aminoacylation for protein translation1.84E-02
134GO:0003333: amino acid transmembrane transport1.97E-02
135GO:0006730: one-carbon metabolic process2.10E-02
136GO:0007005: mitochondrion organization2.10E-02
137GO:0006396: RNA processing2.39E-02
138GO:0045454: cell redox homeostasis2.47E-02
139GO:0080022: primary root development2.65E-02
140GO:0042631: cellular response to water deprivation2.65E-02
141GO:0000226: microtubule cytoskeleton organization2.65E-02
142GO:0048868: pollen tube development2.80E-02
143GO:0009741: response to brassinosteroid2.80E-02
144GO:0008360: regulation of cell shape2.80E-02
145GO:0006814: sodium ion transport2.95E-02
146GO:0009646: response to absence of light2.95E-02
147GO:0032259: methylation3.04E-02
148GO:0019252: starch biosynthetic process3.10E-02
149GO:0008654: phospholipid biosynthetic process3.10E-02
150GO:0009791: post-embryonic development3.10E-02
151GO:0009793: embryo development ending in seed dormancy3.23E-02
152GO:0002229: defense response to oomycetes3.25E-02
153GO:0080156: mitochondrial mRNA modification3.25E-02
154GO:0048235: pollen sperm cell differentiation3.41E-02
155GO:0010286: heat acclimation3.89E-02
156GO:0071805: potassium ion transmembrane transport3.89E-02
157GO:0007623: circadian rhythm4.01E-02
158GO:0001666: response to hypoxia4.23E-02
159GO:0009816: defense response to bacterium, incompatible interaction4.40E-02
160GO:0009627: systemic acquired resistance4.57E-02
161GO:0042128: nitrate assimilation4.57E-02
RankGO TermAdjusted P value
1GO:0042903: tubulin deacetylase activity0.00E+00
2GO:0050278: sedoheptulose-bisphosphatase activity0.00E+00
3GO:0004822: isoleucine-tRNA ligase activity0.00E+00
4GO:0043014: alpha-tubulin binding0.00E+00
5GO:0046905: phytoene synthase activity0.00E+00
6GO:0046408: chlorophyll synthetase activity0.00E+00
7GO:0008942: nitrite reductase [NAD(P)H] activity0.00E+00
8GO:0016767: geranylgeranyl-diphosphate geranylgeranyltransferase activity0.00E+00
9GO:0046608: carotenoid isomerase activity0.00E+00
10GO:0009974: zeinoxanthin epsilon hydroxylase activity0.00E+00
11GO:0050236: pyridoxine:NADP 4-dehydrogenase activity0.00E+00
12GO:0008887: glycerate kinase activity0.00E+00
13GO:0004561: alpha-N-acetylglucosaminidase activity0.00E+00
14GO:0051721: protein phosphatase 2A binding0.00E+00
15GO:0001053: plastid sigma factor activity5.24E-07
16GO:0016987: sigma factor activity5.24E-07
17GO:0004033: aldo-keto reductase (NADP) activity9.59E-06
18GO:0019843: rRNA binding2.00E-05
19GO:0016149: translation release factor activity, codon specific3.75E-05
20GO:0016655: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor6.70E-05
21GO:0004739: pyruvate dehydrogenase (acetyl-transferring) activity6.70E-05
22GO:0005528: FK506 binding1.30E-04
23GO:0045156: electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity2.07E-04
24GO:0003867: 4-aminobutyrate transaminase activity3.24E-04
25GO:0004321: fatty-acyl-CoA synthase activity3.24E-04
26GO:0051996: squalene synthase activity3.24E-04
27GO:0030785: [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity3.24E-04
28GO:0030941: chloroplast targeting sequence binding3.24E-04
29GO:0046912: transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer3.24E-04
30GO:0004807: triose-phosphate isomerase activity3.24E-04
31GO:0050567: glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity3.24E-04
32GO:0009496: plastoquinol--plastocyanin reductase activity3.24E-04
33GO:0046028: electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity3.24E-04
34GO:0003755: peptidyl-prolyl cis-trans isomerase activity3.51E-04
35GO:0003747: translation release factor activity5.01E-04
36GO:0004802: transketolase activity7.07E-04
37GO:0047100: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity7.07E-04
38GO:0004310: farnesyl-diphosphate farnesyltransferase activity7.07E-04
39GO:0008967: phosphoglycolate phosphatase activity7.07E-04
40GO:0004618: phosphoglycerate kinase activity7.07E-04
41GO:0010297: heteropolysaccharide binding7.07E-04
42GO:0004326: tetrahydrofolylpolyglutamate synthase activity7.07E-04
43GO:0004617: phosphoglycerate dehydrogenase activity7.07E-04
44GO:0004047: aminomethyltransferase activity7.07E-04
45GO:0042132: fructose 1,6-bisphosphate 1-phosphatase activity7.07E-04
46GO:0051082: unfolded protein binding7.59E-04
47GO:0016168: chlorophyll binding7.74E-04
48GO:0044183: protein binding involved in protein folding7.96E-04
49GO:0005089: Rho guanyl-nucleotide exchange factor activity7.96E-04
50GO:0031072: heat shock protein binding1.03E-03
51GO:0004222: metalloendopeptidase activity1.14E-03
52GO:0004148: dihydrolipoyl dehydrogenase activity1.15E-03
53GO:0030267: glyoxylate reductase (NADP) activity1.15E-03
54GO:0070402: NADPH binding1.15E-03
55GO:0070330: aromatase activity1.15E-03
56GO:0045158: electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity1.15E-03
57GO:0002161: aminoacyl-tRNA editing activity1.15E-03
58GO:0008266: poly(U) RNA binding1.16E-03
59GO:0031409: pigment binding1.44E-03
60GO:0048487: beta-tubulin binding1.65E-03
61GO:0004300: enoyl-CoA hydratase activity1.65E-03
62GO:0004365: glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity1.65E-03
63GO:0008508: bile acid:sodium symporter activity1.65E-03
64GO:0003878: ATP citrate synthase activity1.65E-03
65GO:0004375: glycine dehydrogenase (decarboxylating) activity1.65E-03
66GO:0015079: potassium ion transmembrane transporter activity1.76E-03
67GO:0051537: 2 iron, 2 sulfur cluster binding2.06E-03
68GO:0005198: structural molecule activity2.17E-03
69GO:0043495: protein anchor2.21E-03
70GO:0004845: uracil phosphoribosyltransferase activity2.21E-03
71GO:0051861: glycolipid binding2.21E-03
72GO:0010328: auxin influx transmembrane transporter activity2.21E-03
73GO:0004607: phosphatidylcholine-sterol O-acyltransferase activity2.21E-03
74GO:0003899: DNA-directed 5'-3' RNA polymerase activity2.73E-03
75GO:0016773: phosphotransferase activity, alcohol group as acceptor2.82E-03
76GO:0018685: alkane 1-monooxygenase activity2.82E-03
77GO:0008374: O-acyltransferase activity2.82E-03
78GO:0050662: coenzyme binding3.39E-03
79GO:0042578: phosphoric ester hydrolase activity3.49E-03
80GO:0090447: glycerol-3-phosphate 2-O-acyltransferase activity3.49E-03
81GO:0080030: methyl indole-3-acetate esterase activity3.49E-03
82GO:0004332: fructose-bisphosphate aldolase activity3.49E-03
83GO:0048038: quinone binding3.89E-03
84GO:0004723: calcium-dependent protein serine/threonine phosphatase activity4.20E-03
85GO:0004849: uridine kinase activity4.20E-03
86GO:0004616: phosphogluconate dehydrogenase (decarboxylating) activity4.20E-03
87GO:0005525: GTP binding4.33E-03
88GO:0019899: enzyme binding4.95E-03
89GO:0005509: calcium ion binding5.56E-03
90GO:0003843: 1,3-beta-D-glucan synthase activity6.60E-03
91GO:0032041: NAD-dependent histone deacetylase activity (H3-K14 specific)6.60E-03
92GO:0016207: 4-coumarate-CoA ligase activity7.48E-03
93GO:0015238: drug transmembrane transporter activity7.73E-03
94GO:0047372: acylglycerol lipase activity1.04E-02
95GO:0015386: potassium:proton antiporter activity1.04E-02
96GO:0016787: hydrolase activity1.07E-02
97GO:0016491: oxidoreductase activity1.11E-02
98GO:0000049: tRNA binding1.14E-02
99GO:0004364: glutathione transferase activity1.16E-02
100GO:0004022: alcohol dehydrogenase (NAD) activity1.25E-02
101GO:0004089: carbonate dehydratase activity1.25E-02
102GO:0042973: glucan endo-1,3-beta-D-glucosidase activity1.36E-02
103GO:0008168: methyltransferase activity1.43E-02
104GO:0051287: NAD binding1.46E-02
105GO:0051536: iron-sulfur cluster binding1.72E-02
106GO:0004407: histone deacetylase activity1.72E-02
107GO:0043424: protein histidine kinase binding1.84E-02
108GO:0004176: ATP-dependent peptidase activity1.97E-02
109GO:0019706: protein-cysteine S-palmitoyltransferase activity1.97E-02
110GO:0016874: ligase activity2.19E-02
111GO:0022891: substrate-specific transmembrane transporter activity2.23E-02
112GO:0003756: protein disulfide isomerase activity2.37E-02
113GO:0016746: transferase activity, transferring acyl groups2.39E-02
114GO:0004812: aminoacyl-tRNA ligase activity2.51E-02
115GO:0003924: GTPase activity3.20E-02
116GO:0003723: RNA binding3.47E-02
117GO:0016671: oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor3.57E-02
118GO:0016791: phosphatase activity3.73E-02
119GO:0016759: cellulose synthase activity3.73E-02
120GO:0015297: antiporter activity3.83E-02
121GO:0008237: metallopeptidase activity3.89E-02
122GO:0005200: structural constituent of cytoskeleton3.89E-02
123GO:0008483: transaminase activity3.89E-02
124GO:0016597: amino acid binding4.06E-02
125GO:0009931: calcium-dependent protein serine/threonine kinase activity4.57E-02
126GO:0004683: calmodulin-dependent protein kinase activity4.75E-02
127GO:0000982: transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding4.92E-02
RankGO TermAdjusted P value
1GO:0009344: nitrite reductase complex [NAD(P)H]0.00E+00
2GO:0009571: proplastid stroma0.00E+00
3GO:0009507: chloroplast9.71E-58
4GO:0009535: chloroplast thylakoid membrane8.87E-30
5GO:0009941: chloroplast envelope1.35E-25
6GO:0009570: chloroplast stroma2.40E-25
7GO:0009543: chloroplast thylakoid lumen7.30E-12
8GO:0010598: NAD(P)H dehydrogenase complex (plastoquinone)1.93E-11
9GO:0009579: thylakoid3.92E-11
10GO:0009534: chloroplast thylakoid5.18E-10
11GO:0009654: photosystem II oxygen evolving complex2.50E-09
12GO:0030095: chloroplast photosystem II4.13E-08
13GO:0019898: extrinsic component of membrane1.18E-06
14GO:0031969: chloroplast membrane3.81E-06
15GO:0042651: thylakoid membrane6.33E-06
16GO:0031977: thylakoid lumen2.14E-05
17GO:0010319: stromule5.72E-05
18GO:0009706: chloroplast inner membrane1.12E-04
19GO:0010287: plastoglobule1.60E-04
20GO:0016020: membrane2.42E-04
21GO:0009536: plastid3.18E-04
22GO:0009547: plastid ribosome3.24E-04
23GO:0009782: photosystem I antenna complex3.24E-04
24GO:0030956: glutamyl-tRNA(Gln) amidotransferase complex3.24E-04
25GO:0009523: photosystem II4.13E-04
26GO:0045298: tubulin complex5.01E-04
27GO:0000427: plastid-encoded plastid RNA polymerase complex7.07E-04
28GO:0030981: cortical microtubule cytoskeleton7.07E-04
29GO:0030076: light-harvesting complex1.29E-03
30GO:0009346: citrate lyase complex1.65E-03
31GO:0005960: glycine cleavage complex1.65E-03
32GO:0046658: anchored component of plasma membrane2.66E-03
33GO:0009512: cytochrome b6f complex2.82E-03
34GO:0031359: integral component of chloroplast outer membrane4.95E-03
35GO:0009533: chloroplast stromal thylakoid4.95E-03
36GO:0048046: apoplast5.40E-03
37GO:0009539: photosystem II reaction center6.60E-03
38GO:0000148: 1,3-beta-D-glucan synthase complex6.60E-03
39GO:0005840: ribosome7.14E-03
40GO:0005759: mitochondrial matrix7.61E-03
41GO:0016324: apical plasma membrane9.37E-03
42GO:0005886: plasma membrane1.03E-02
43GO:0000311: plastid large ribosomal subunit1.14E-02
44GO:0009508: plastid chromosome1.25E-02
45GO:0030659: cytoplasmic vesicle membrane1.36E-02
46GO:0043234: protein complex1.60E-02
47GO:0009532: plastid stroma1.97E-02
48GO:0009522: photosystem I2.95E-02
49GO:0009295: nucleoid3.89E-02
50GO:0030529: intracellular ribonucleoprotein complex4.23E-02
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Gene type



Gene DE type