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

AT4G39960

GO-BP
GO-MF
GO-CC
RankGO TermAdjusted P value
1GO:0006428: isoleucyl-tRNA aminoacylation0.00E+00
2GO:0005996: monosaccharide metabolic process0.00E+00
3GO:0015717: triose phosphate transport0.00E+00
4GO:0046471: phosphatidylglycerol metabolic process0.00E+00
5GO:0018023: peptidyl-lysine trimethylation0.00E+00
6GO:0052865: 1-deoxy-D-xylulose 5-phosphate biosynthetic process0.00E+00
7GO:1905157: positive regulation of photosynthesis0.00E+00
8GO:0000476: maturation of 4.5S rRNA0.00E+00
9GO:1901918: negative regulation of exoribonuclease activity0.00E+00
10GO:0000967: rRNA 5'-end processing0.00E+00
11GO:0006780: uroporphyrinogen III biosynthetic process0.00E+00
12GO:0033614: chloroplast proton-transporting ATP synthase complex assembly0.00E+00
13GO:0015995: chlorophyll biosynthetic process1.16E-09
14GO:0015979: photosynthesis3.35E-08
15GO:0009773: photosynthetic electron transport in photosystem I4.39E-08
16GO:0010207: photosystem II assembly1.42E-07
17GO:0019288: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway5.06E-06
18GO:0034470: ncRNA processing8.58E-06
19GO:0032544: plastid translation2.90E-05
20GO:0090391: granum assembly2.96E-05
21GO:0010258: NADH dehydrogenase complex (plastoquinone) assembly6.40E-05
22GO:0071484: cellular response to light intensity6.40E-05
23GO:0010114: response to red light7.26E-05
24GO:0015994: chlorophyll metabolic process1.12E-04
25GO:0006094: gluconeogenesis1.27E-04
26GO:0009643: photosynthetic acclimation2.46E-04
27GO:0042549: photosystem II stabilization2.46E-04
28GO:0009768: photosynthesis, light harvesting in photosystem I2.80E-04
29GO:1901259: chloroplast rRNA processing3.30E-04
30GO:0010196: nonphotochemical quenching4.25E-04
31GO:0080112: seed growth4.40E-04
32GO:0005980: glycogen catabolic process4.40E-04
33GO:0010028: xanthophyll cycle4.40E-04
34GO:0034337: RNA folding4.40E-04
35GO:0009090: homoserine biosynthetic process4.40E-04
36GO:1905039: carboxylic acid transmembrane transport4.40E-04
37GO:1905200: gibberellic acid transmembrane transport4.40E-04
38GO:0006353: DNA-templated transcription, termination5.32E-04
39GO:0009657: plastid organization6.48E-04
40GO:0055114: oxidation-reduction process6.54E-04
41GO:0006098: pentose-phosphate shunt7.77E-04
42GO:0018026: peptidyl-lysine monomethylation9.50E-04
43GO:0006898: receptor-mediated endocytosis9.50E-04
44GO:0071457: cellular response to ozone9.50E-04
45GO:0016122: xanthophyll metabolic process9.50E-04
46GO:0030388: fructose 1,6-bisphosphate metabolic process9.50E-04
47GO:0010270: photosystem II oxygen evolving complex assembly9.50E-04
48GO:0006782: protoporphyrinogen IX biosynthetic process1.06E-03
49GO:0032259: methylation1.18E-03
50GO:0018119: peptidyl-cysteine S-nitrosylation1.23E-03
51GO:0006518: peptide metabolic process1.55E-03
52GO:0009405: pathogenesis1.55E-03
53GO:0035436: triose phosphate transmembrane transport1.55E-03
54GO:0006696: ergosterol biosynthetic process1.55E-03
55GO:0006000: fructose metabolic process1.55E-03
56GO:0019253: reductive pentose-phosphate cycle1.80E-03
57GO:0010731: protein glutathionylation2.24E-03
58GO:0006168: adenine salvage2.24E-03
59GO:0009067: aspartate family amino acid biosynthetic process2.24E-03
60GO:1902358: sulfate transmembrane transport2.24E-03
61GO:0045338: farnesyl diphosphate metabolic process2.24E-03
62GO:0006166: purine ribonucleoside salvage2.24E-03
63GO:0006020: inositol metabolic process2.24E-03
64GO:0051085: chaperone mediated protein folding requiring cofactor2.24E-03
65GO:0009152: purine ribonucleotide biosynthetic process2.24E-03
66GO:0010601: positive regulation of auxin biosynthetic process2.24E-03
67GO:0046653: tetrahydrofolate metabolic process2.24E-03
68GO:0009052: pentose-phosphate shunt, non-oxidative branch2.24E-03
69GO:0009853: photorespiration2.41E-03
70GO:0006021: inositol biosynthetic process3.01E-03
71GO:0071483: cellular response to blue light3.01E-03
72GO:0015713: phosphoglycerate transport3.01E-03
73GO:0071486: cellular response to high light intensity3.01E-03
74GO:0019464: glycine decarboxylation via glycine cleavage system3.01E-03
75GO:0009765: photosynthesis, light harvesting3.01E-03
76GO:0010107: potassium ion import3.01E-03
77GO:0045727: positive regulation of translation3.01E-03
78GO:0016114: terpenoid biosynthetic process3.03E-03
79GO:0061077: chaperone-mediated protein folding3.03E-03
80GO:0071493: cellular response to UV-B3.85E-03
81GO:0098719: sodium ion import across plasma membrane3.85E-03
82GO:0006564: L-serine biosynthetic process3.85E-03
83GO:0009904: chloroplast accumulation movement3.85E-03
84GO:0006656: phosphatidylcholine biosynthetic process3.85E-03
85GO:0044209: AMP salvage3.85E-03
86GO:0009409: response to cold3.95E-03
87GO:0010190: cytochrome b6f complex assembly4.77E-03
88GO:0006828: manganese ion transport4.77E-03
89GO:0009228: thiamine biosynthetic process4.77E-03
90GO:0046855: inositol phosphate dephosphorylation4.77E-03
91GO:0010304: PSII associated light-harvesting complex II catabolic process4.77E-03
92GO:0006751: glutathione catabolic process4.77E-03
93GO:1902456: regulation of stomatal opening4.77E-03
94GO:0006364: rRNA processing4.87E-03
95GO:0019252: starch biosynthetic process5.73E-03
96GO:0042026: protein refolding5.75E-03
97GO:0009903: chloroplast avoidance movement5.75E-03
98GO:0009854: oxidative photosynthetic carbon pathway5.75E-03
99GO:0009088: threonine biosynthetic process5.75E-03
100GO:0009955: adaxial/abaxial pattern specification5.75E-03
101GO:0071333: cellular response to glucose stimulus5.75E-03
102GO:0006096: glycolytic process6.03E-03
103GO:0032502: developmental process6.56E-03
104GO:0009658: chloroplast organization6.78E-03
105GO:0048437: floral organ development6.80E-03
106GO:0009645: response to low light intensity stimulus6.80E-03
107GO:0008272: sulfate transport6.80E-03
108GO:0009769: photosynthesis, light harvesting in photosystem II6.80E-03
109GO:0009772: photosynthetic electron transport in photosystem II6.80E-03
110GO:0042254: ribosome biogenesis6.97E-03
111GO:1901657: glycosyl compound metabolic process7.00E-03
112GO:0009642: response to light intensity7.91E-03
113GO:0010078: maintenance of root meristem identity7.91E-03
114GO:0042255: ribosome assembly7.91E-03
115GO:0055075: potassium ion homeostasis7.91E-03
116GO:0052543: callose deposition in cell wall7.91E-03
117GO:0010027: thylakoid membrane organization8.90E-03
118GO:0043562: cellular response to nitrogen levels9.09E-03
119GO:0006002: fructose 6-phosphate metabolic process9.09E-03
120GO:0015996: chlorophyll catabolic process9.09E-03
121GO:0019430: removal of superoxide radicals9.09E-03
122GO:0090333: regulation of stomatal closure1.03E-02
123GO:0006783: heme biosynthetic process1.03E-02
124GO:0006754: ATP biosynthetic process1.03E-02
125GO:0009821: alkaloid biosynthetic process1.03E-02
126GO:0010206: photosystem II repair1.03E-02
127GO:0009086: methionine biosynthetic process1.16E-02
128GO:0051453: regulation of intracellular pH1.16E-02
129GO:0005982: starch metabolic process1.16E-02
130GO:0031146: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process1.16E-02
131GO:0006779: porphyrin-containing compound biosynthetic process1.16E-02
132GO:0018298: protein-chromophore linkage1.17E-02
133GO:0009813: flavonoid biosynthetic process1.22E-02
134GO:0006810: transport1.28E-02
135GO:0010218: response to far red light1.29E-02
136GO:0009641: shade avoidance1.30E-02
137GO:0006949: syncytium formation1.30E-02
138GO:0072593: reactive oxygen species metabolic process1.44E-02
139GO:0043085: positive regulation of catalytic activity1.44E-02
140GO:0000272: polysaccharide catabolic process1.44E-02
141GO:0015770: sucrose transport1.44E-02
142GO:0006415: translational termination1.44E-02
143GO:0009684: indoleacetic acid biosynthetic process1.44E-02
144GO:0006816: calcium ion transport1.44E-02
145GO:0009089: lysine biosynthetic process via diaminopimelate1.44E-02
146GO:0046686: response to cadmium ion1.45E-02
147GO:0009637: response to blue light1.48E-02
148GO:0034599: cellular response to oxidative stress1.55E-02
149GO:0005983: starch catabolic process1.58E-02
150GO:0016024: CDP-diacylglycerol biosynthetic process1.58E-02
151GO:0006790: sulfur compound metabolic process1.58E-02
152GO:0018107: peptidyl-threonine phosphorylation1.73E-02
153GO:0005986: sucrose biosynthetic process1.73E-02
154GO:0010588: cotyledon vascular tissue pattern formation1.73E-02
155GO:0007015: actin filament organization1.89E-02
156GO:0010223: secondary shoot formation1.89E-02
157GO:0048467: gynoecium development1.89E-02
158GO:0010143: cutin biosynthetic process1.89E-02
159GO:0009901: anther dehiscence2.05E-02
160GO:0005985: sucrose metabolic process2.05E-02
161GO:0046854: phosphatidylinositol phosphorylation2.05E-02
162GO:0006636: unsaturated fatty acid biosynthetic process2.21E-02
163GO:0051017: actin filament bundle assembly2.38E-02
164GO:0006418: tRNA aminoacylation for protein translation2.55E-02
165GO:0019915: lipid storage2.73E-02
166GO:0009269: response to desiccation2.73E-02
167GO:0030433: ubiquitin-dependent ERAD pathway2.91E-02
168GO:0007005: mitochondrion organization2.91E-02
169GO:0016226: iron-sulfur cluster assembly2.91E-02
170GO:0071215: cellular response to abscisic acid stimulus3.10E-02
171GO:0048367: shoot system development3.15E-02
172GO:0009306: protein secretion3.29E-02
173GO:0005975: carbohydrate metabolic process3.47E-02
174GO:0009735: response to cytokinin3.47E-02
175GO:0016117: carotenoid biosynthetic process3.48E-02
176GO:0080167: response to karrikin3.49E-02
177GO:0080022: primary root development3.68E-02
178GO:0000413: protein peptidyl-prolyl isomerization3.68E-02
179GO:0010087: phloem or xylem histogenesis3.68E-02
180GO:0042631: cellular response to water deprivation3.68E-02
181GO:0006396: RNA processing3.78E-02
182GO:0071472: cellular response to salt stress3.88E-02
183GO:0006662: glycerol ether metabolic process3.88E-02
184GO:0009741: response to brassinosteroid3.88E-02
185GO:0009958: positive gravitropism3.88E-02
186GO:0006885: regulation of pH3.88E-02
187GO:0009416: response to light stimulus3.94E-02
188GO:0015986: ATP synthesis coupled proton transport4.09E-02
189GO:0006814: sodium ion transport4.09E-02
190GO:0048825: cotyledon development4.30E-02
191GO:0009556: microsporogenesis4.30E-02
192GO:0009851: auxin biosynthetic process4.30E-02
193GO:0009630: gravitropism4.73E-02
194GO:0009058: biosynthetic process4.83E-02
RankGO TermAdjusted P value
1GO:0047538: 2-carboxy-D-arabinitol-1-phosphatase activity0.00E+00
2GO:0050518: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity0.00E+00
3GO:0051060: pullulanase activity0.00E+00
4GO:0004822: isoleucine-tRNA ligase activity0.00E+00
5GO:0046408: chlorophyll synthetase activity0.00E+00
6GO:0004852: uroporphyrinogen-III synthase activity0.00E+00
7GO:0008942: nitrite reductase [NAD(P)H] activity0.00E+00
8GO:0035798: 2-alkenal reductase (NADP+) activity0.00E+00
9GO:0004318: enoyl-[acyl-carrier-protein] reductase (NADH) activity0.00E+00
10GO:0052637: delta 3-trans-hexadecenoic acid phosphatidylglycerol desaturase activity0.00E+00
11GO:0016631: enoyl-[acyl-carrier-protein] reductase activity0.00E+00
12GO:0052667: phosphomethylethanolamine N-methyltransferase activity0.00E+00
13GO:0090711: FMN hydrolase activity0.00E+00
14GO:0050515: 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity0.00E+00
15GO:0010303: limit dextrinase activity0.00E+00
16GO:0008887: glycerate kinase activity0.00E+00
17GO:0046422: violaxanthin de-epoxidase activity0.00E+00
18GO:0019843: rRNA binding5.18E-07
19GO:0003755: peptidyl-prolyl cis-trans isomerase activity1.02E-04
20GO:0016655: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor1.12E-04
21GO:0031409: pigment binding2.11E-04
22GO:0005528: FK506 binding2.44E-04
23GO:0004332: fructose-bisphosphate aldolase activity2.46E-04
24GO:0034256: chlorophyll(ide) b reductase activity4.40E-04
25GO:0004853: uroporphyrinogen decarboxylase activity4.40E-04
26GO:0030785: [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity4.40E-04
27GO:0045486: naringenin 3-dioxygenase activity4.40E-04
28GO:0035671: enone reductase activity4.40E-04
29GO:0008886: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity4.40E-04
30GO:1905201: gibberellin transmembrane transporter activity4.40E-04
31GO:0008184: glycogen phosphorylase activity4.40E-04
32GO:0004856: xylulokinase activity4.40E-04
33GO:0004645: phosphorylase activity4.40E-04
34GO:0008934: inositol monophosphate 1-phosphatase activity9.50E-04
35GO:0052833: inositol monophosphate 4-phosphatase activity9.50E-04
36GO:0004412: homoserine dehydrogenase activity9.50E-04
37GO:0004310: farnesyl-diphosphate farnesyltransferase activity9.50E-04
38GO:0000234: phosphoethanolamine N-methyltransferase activity9.50E-04
39GO:0008967: phosphoglycolate phosphatase activity9.50E-04
40GO:0047746: chlorophyllase activity9.50E-04
41GO:0004618: phosphoglycerate kinase activity9.50E-04
42GO:0010297: heteropolysaccharide binding9.50E-04
43GO:0003839: gamma-glutamylcyclotransferase activity9.50E-04
44GO:0050362: L-tryptophan:2-oxoglutarate aminotransferase activity9.50E-04
45GO:0004617: phosphoglycerate dehydrogenase activity9.50E-04
46GO:0008661: 1-deoxy-D-xylulose-5-phosphate synthase activity9.50E-04
47GO:0052832: inositol monophosphate 3-phosphatase activity9.50E-04
48GO:0033201: alpha-1,4-glucan synthase activity9.50E-04
49GO:0042132: fructose 1,6-bisphosphate 1-phosphatase activity9.50E-04
50GO:0018708: thiol S-methyltransferase activity9.50E-04
51GO:0080097: L-tryptophan:pyruvate aminotransferase activity9.50E-04
52GO:0016630: protochlorophyllide reductase activity9.50E-04
53GO:0015386: potassium:proton antiporter activity1.23E-03
54GO:0016491: oxidoreductase activity1.30E-03
55GO:0016168: chlorophyll binding1.36E-03
56GO:0008168: methyltransferase activity1.53E-03
57GO:0002161: aminoacyl-tRNA editing activity1.55E-03
58GO:0004751: ribose-5-phosphate isomerase activity1.55E-03
59GO:0045174: glutathione dehydrogenase (ascorbate) activity1.55E-03
60GO:0016742: hydroxymethyl-, formyl- and related transferase activity1.55E-03
61GO:0071917: triose-phosphate transmembrane transporter activity1.55E-03
62GO:0008864: formyltetrahydrofolate deformylase activity1.55E-03
63GO:0010277: chlorophyllide a oxygenase [overall] activity1.55E-03
64GO:0090729: toxin activity1.55E-03
65GO:0004373: glycogen (starch) synthase activity1.55E-03
66GO:0016149: translation release factor activity, codon specific2.24E-03
67GO:0022890: inorganic cation transmembrane transporter activity2.24E-03
68GO:0016851: magnesium chelatase activity2.24E-03
69GO:0004072: aspartate kinase activity2.24E-03
70GO:0004375: glycine dehydrogenase (decarboxylating) activity2.24E-03
71GO:0019201: nucleotide kinase activity2.24E-03
72GO:0003999: adenine phosphoribosyltransferase activity2.24E-03
73GO:0015120: phosphoglycerate transmembrane transporter activity3.01E-03
74GO:0016279: protein-lysine N-methyltransferase activity3.01E-03
75GO:0045430: chalcone isomerase activity3.01E-03
76GO:0009011: starch synthase activity3.01E-03
77GO:0051537: 2 iron, 2 sulfur cluster binding3.68E-03
78GO:0016773: phosphotransferase activity, alcohol group as acceptor3.85E-03
79GO:0003959: NADPH dehydrogenase activity3.85E-03
80GO:0016846: carbon-sulfur lyase activity3.85E-03
81GO:0003727: single-stranded RNA binding3.93E-03
82GO:0004556: alpha-amylase activity4.77E-03
83GO:0004366: glycerol-3-phosphate O-acyltransferase activity4.77E-03
84GO:0004784: superoxide dismutase activity4.77E-03
85GO:0015081: sodium ion transmembrane transporter activity4.77E-03
86GO:0090447: glycerol-3-phosphate 2-O-acyltransferase activity4.77E-03
87GO:0004629: phospholipase C activity4.77E-03
88GO:0004435: phosphatidylinositol phospholipase C activity5.75E-03
89GO:0004017: adenylate kinase activity5.75E-03
90GO:0008441: 3'(2'),5'-bisphosphate nucleotidase activity5.75E-03
91GO:0048038: quinone binding6.14E-03
92GO:0004525: ribonuclease III activity7.91E-03
93GO:0016597: amino acid binding8.40E-03
94GO:0008271: secondary active sulfate transmembrane transporter activity9.09E-03
95GO:0003747: translation release factor activity1.03E-02
96GO:0102483: scopolin beta-glucosidase activity1.05E-02
97GO:0005384: manganese ion transmembrane transporter activity1.16E-02
98GO:0016844: strictosidine synthase activity1.16E-02
99GO:0004028: 3-chloroallyl aldehyde dehydrogenase activity1.16E-02
100GO:0004222: metalloendopeptidase activity1.29E-02
101GO:0030234: enzyme regulator activity1.30E-02
102GO:0008047: enzyme activator activity1.30E-02
103GO:0008559: xenobiotic-transporting ATPase activity1.44E-02
104GO:0044183: protein binding involved in protein folding1.44E-02
105GO:0047372: acylglycerol lipase activity1.44E-02
106GO:0008515: sucrose transmembrane transporter activity1.44E-02
107GO:0000049: tRNA binding1.58E-02
108GO:0015116: sulfate transmembrane transporter activity1.58E-02
109GO:0008422: beta-glucosidase activity1.62E-02
110GO:0004022: alcohol dehydrogenase (NAD) activity1.73E-02
111GO:0015095: magnesium ion transmembrane transporter activity1.73E-02
112GO:0003725: double-stranded RNA binding1.73E-02
113GO:0042973: glucan endo-1,3-beta-D-glucosidase activity1.89E-02
114GO:0008266: poly(U) RNA binding1.89E-02
115GO:0051119: sugar transmembrane transporter activity2.05E-02
116GO:0043621: protein self-association2.07E-02
117GO:0051536: iron-sulfur cluster binding2.38E-02
118GO:0031418: L-ascorbic acid binding2.38E-02
119GO:0003735: structural constituent of ribosome2.41E-02
120GO:0015079: potassium ion transmembrane transporter activity2.55E-02
121GO:0016787: hydrolase activity2.80E-02
122GO:0047134: protein-disulfide reductase activity3.48E-02
123GO:0004812: aminoacyl-tRNA ligase activity3.48E-02
124GO:0046933: proton-transporting ATP synthase activity, rotational mechanism3.88E-02
125GO:0015299: solute:proton antiporter activity4.09E-02
126GO:0050662: coenzyme binding4.09E-02
127GO:0004791: thioredoxin-disulfide reductase activity4.09E-02
128GO:0016705: oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen4.71E-02
129GO:0015385: sodium:proton antiporter activity4.94E-02
130GO:0016671: oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor4.94E-02
131GO:0051015: actin filament binding4.94E-02
RankGO TermAdjusted P value
1GO:0009575: chromoplast stroma0.00E+00
2GO:0009571: proplastid stroma0.00E+00
3GO:0005835: fatty acid synthase complex0.00E+00
4GO:0009507: chloroplast3.31E-58
5GO:0009535: chloroplast thylakoid membrane9.05E-35
6GO:0009534: chloroplast thylakoid7.28E-32
7GO:0009570: chloroplast stroma1.02E-26
8GO:0009941: chloroplast envelope3.94E-21
9GO:0009579: thylakoid5.90E-20
10GO:0009543: chloroplast thylakoid lumen1.52E-13
11GO:0031977: thylakoid lumen3.56E-13
12GO:0031969: chloroplast membrane1.24E-09
13GO:0010598: NAD(P)H dehydrogenase complex (plastoquinone)9.80E-09
14GO:0010287: plastoglobule5.71E-06
15GO:0010319: stromule8.96E-06
16GO:0030076: light-harvesting complex1.80E-04
17GO:0009654: photosystem II oxygen evolving complex2.80E-04
18GO:0042651: thylakoid membrane2.80E-04
19GO:0009515: granal stacked thylakoid4.40E-04
20GO:0009547: plastid ribosome4.40E-04
21GO:0005840: ribosome7.24E-04
22GO:0019898: extrinsic component of membrane7.33E-04
23GO:0000427: plastid-encoded plastid RNA polymerase complex9.50E-04
24GO:0010007: magnesium chelatase complex1.55E-03
25GO:0033281: TAT protein transport complex1.55E-03
26GO:0030095: chloroplast photosystem II1.80E-03
27GO:0005960: glycine cleavage complex2.24E-03
28GO:0009517: PSII associated light-harvesting complex II3.01E-03
29GO:0009544: chloroplast ATP synthase complex3.01E-03
30GO:0045261: proton-transporting ATP synthase complex, catalytic core F(1)4.77E-03
31GO:0009522: photosystem I5.34E-03
32GO:0009523: photosystem II5.73E-03
33GO:0009840: chloroplastic endopeptidase Clp complex5.75E-03
34GO:0009501: amyloplast7.91E-03
35GO:0031982: vesicle7.91E-03
36GO:0005763: mitochondrial small ribosomal subunit1.03E-02
37GO:0000311: plastid large ribosomal subunit1.58E-02
38GO:0032040: small-subunit processome1.58E-02
39GO:0048046: apoplast1.70E-02
40GO:0009508: plastid chromosome1.73E-02
41GO:0015935: small ribosomal subunit2.73E-02
42GO:0009532: plastid stroma2.73E-02
43GO:0015629: actin cytoskeleton3.10E-02
44GO:0009706: chloroplast inner membrane3.67E-02
45GO:0005623: cell4.71E-02
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Gene type



Gene DE type