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

AT3G56650

GO-BP
GO-MF
GO-CC
RankGO TermAdjusted P value
1GO:0002184: cytoplasmic translational termination0.00E+00
2GO:0032194: ubiquinone biosynthetic process via 3,4-dihydroxy-5-polyprenylbenzoate0.00E+00
3GO:0006780: uroporphyrinogen III biosynthetic process0.00E+00
4GO:0090071: negative regulation of ribosome biogenesis0.00E+00
5GO:0070681: glutaminyl-tRNAGln biosynthesis via transamidation0.00E+00
6GO:0033494: ferulate metabolic process0.00E+00
7GO:0061635: regulation of protein complex stability0.00E+00
8GO:0006223: uracil salvage0.00E+00
9GO:0016553: base conversion or substitution editing0.00E+00
10GO:0042493: response to drug0.00E+00
11GO:0006399: tRNA metabolic process0.00E+00
12GO:0034337: RNA folding0.00E+00
13GO:0006412: translation3.11E-15
14GO:0015979: photosynthesis4.60E-14
15GO:0032544: plastid translation4.89E-14
16GO:0015995: chlorophyll biosynthetic process5.41E-12
17GO:0009735: response to cytokinin9.65E-12
18GO:0010027: thylakoid membrane organization4.80E-09
19GO:0042254: ribosome biogenesis1.27E-08
20GO:0090391: granum assembly4.22E-08
21GO:0010207: photosystem II assembly2.76E-06
22GO:0010196: nonphotochemical quenching7.14E-06
23GO:0010206: photosystem II repair2.13E-05
24GO:0009658: chloroplast organization2.24E-05
25GO:0009773: photosynthetic electron transport in photosystem I4.72E-05
26GO:0009772: photosynthetic electron transport in photosystem II2.89E-04
27GO:0071588: hydrogen peroxide mediated signaling pathway3.40E-04
28GO:0043489: RNA stabilization3.40E-04
29GO:1904966: positive regulation of vitamin E biosynthetic process3.40E-04
30GO:0000481: maturation of 5S rRNA3.40E-04
31GO:1904964: positive regulation of phytol biosynthetic process3.40E-04
32GO:0042371: vitamin K biosynthetic process3.40E-04
33GO:0008610: lipid biosynthetic process3.64E-04
34GO:0009657: plastid organization4.45E-04
35GO:0006779: porphyrin-containing compound biosynthetic process6.32E-04
36GO:0006782: protoporphyrinogen IX biosynthetic process7.37E-04
37GO:0010024: phytochromobilin biosynthetic process7.40E-04
38GO:1902326: positive regulation of chlorophyll biosynthetic process7.40E-04
39GO:0006729: tetrahydrobiopterin biosynthetic process7.40E-04
40GO:0006568: tryptophan metabolic process7.40E-04
41GO:0043085: positive regulation of catalytic activity8.49E-04
42GO:0016024: CDP-diacylglycerol biosynthetic process9.69E-04
43GO:0006006: glucose metabolic process1.10E-03
44GO:0010581: regulation of starch biosynthetic process1.20E-03
45GO:0006788: heme oxidation1.20E-03
46GO:0006518: peptide metabolic process1.20E-03
47GO:0006617: SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition1.20E-03
48GO:0080055: low-affinity nitrate transport1.20E-03
49GO:0051604: protein maturation1.20E-03
50GO:0010143: cutin biosynthetic process1.23E-03
51GO:0071484: cellular response to light intensity1.72E-03
52GO:0051085: chaperone mediated protein folding requiring cofactor1.72E-03
53GO:0051639: actin filament network formation1.72E-03
54GO:0006241: CTP biosynthetic process1.72E-03
55GO:0080170: hydrogen peroxide transmembrane transport1.72E-03
56GO:0009052: pentose-phosphate shunt, non-oxidative branch1.72E-03
57GO:0009650: UV protection1.72E-03
58GO:0006165: nucleoside diphosphate phosphorylation1.72E-03
59GO:0006228: UTP biosynthetic process1.72E-03
60GO:0006424: glutamyl-tRNA aminoacylation1.72E-03
61GO:1901332: negative regulation of lateral root development1.72E-03
62GO:0006986: response to unfolded protein1.72E-03
63GO:0080158: chloroplast ribulose bisphosphate carboxylase complex biogenesis1.72E-03
64GO:2001141: regulation of RNA biosynthetic process1.72E-03
65GO:0051513: regulation of monopolar cell growth1.72E-03
66GO:0009793: embryo development ending in seed dormancy2.03E-03
67GO:0051764: actin crosslink formation2.31E-03
68GO:0006183: GTP biosynthetic process2.31E-03
69GO:0045727: positive regulation of translation2.31E-03
70GO:0030104: water homeostasis2.31E-03
71GO:0044206: UMP salvage2.31E-03
72GO:0019287: isopentenyl diphosphate biosynthetic process, mevalonate pathway2.31E-03
73GO:0009411: response to UV2.46E-03
74GO:0000304: response to singlet oxygen2.96E-03
75GO:0043097: pyrimidine nucleoside salvage2.96E-03
76GO:0032543: mitochondrial translation2.96E-03
77GO:0010236: plastoquinone biosynthetic process2.96E-03
78GO:0045038: protein import into chloroplast thylakoid membrane2.96E-03
79GO:0006461: protein complex assembly2.96E-03
80GO:0042335: cuticle development3.13E-03
81GO:0000413: protein peptidyl-prolyl isomerization3.13E-03
82GO:0019288: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway3.65E-03
83GO:0000470: maturation of LSU-rRNA3.65E-03
84GO:0006655: phosphatidylglycerol biosynthetic process3.65E-03
85GO:0006206: pyrimidine nucleobase metabolic process3.65E-03
86GO:0042549: photosystem II stabilization3.65E-03
87GO:0042372: phylloquinone biosynthetic process4.40E-03
88GO:1901259: chloroplast rRNA processing4.40E-03
89GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)4.40E-03
90GO:0017148: negative regulation of translation4.40E-03
91GO:0009854: oxidative photosynthetic carbon pathway4.40E-03
92GO:0010019: chloroplast-nucleus signaling pathway4.40E-03
93GO:0006614: SRP-dependent cotranslational protein targeting to membrane5.19E-03
94GO:1900057: positive regulation of leaf senescence5.19E-03
95GO:0006400: tRNA modification5.19E-03
96GO:0048564: photosystem I assembly6.03E-03
97GO:0030091: protein repair6.03E-03
98GO:0006605: protein targeting6.03E-03
99GO:0032508: DNA duplex unwinding6.03E-03
100GO:0010492: maintenance of shoot apical meristem identity6.03E-03
101GO:0045454: cell redox homeostasis6.84E-03
102GO:0071482: cellular response to light stimulus6.92E-03
103GO:0019430: removal of superoxide radicals6.92E-03
104GO:0009051: pentose-phosphate shunt, oxidative branch7.85E-03
105GO:0048507: meristem development7.85E-03
106GO:0018298: protein-chromophore linkage7.88E-03
107GO:0010380: regulation of chlorophyll biosynthetic process8.82E-03
108GO:0009631: cold acclimation9.11E-03
109GO:0045490: pectin catabolic process9.37E-03
110GO:0009451: RNA modification9.65E-03
111GO:0006535: cysteine biosynthetic process from serine9.84E-03
112GO:0048829: root cap development9.84E-03
113GO:0045036: protein targeting to chloroplast9.84E-03
114GO:0009637: response to blue light1.00E-02
115GO:0006457: protein folding1.03E-02
116GO:0034599: cellular response to oxidative stress1.05E-02
117GO:0009073: aromatic amino acid family biosynthetic process1.09E-02
118GO:0006415: translational termination1.09E-02
119GO:0006352: DNA-templated transcription, initiation1.09E-02
120GO:0008152: metabolic process1.09E-02
121GO:0018119: peptidyl-cysteine S-nitrosylation1.09E-02
122GO:0010114: response to red light1.29E-02
123GO:0009409: response to cold1.34E-02
124GO:0019253: reductive pentose-phosphate cycle1.43E-02
125GO:0009734: auxin-activated signaling pathway1.58E-02
126GO:0019344: cysteine biosynthetic process1.80E-02
127GO:0009116: nucleoside metabolic process1.80E-02
128GO:0000027: ribosomal large subunit assembly1.80E-02
129GO:0051017: actin filament bundle assembly1.80E-02
130GO:0009768: photosynthesis, light harvesting in photosystem I1.93E-02
131GO:0031408: oxylipin biosynthetic process2.07E-02
132GO:0016114: terpenoid biosynthetic process2.07E-02
133GO:0003333: amino acid transmembrane transport2.07E-02
134GO:0035428: hexose transmembrane transport2.21E-02
135GO:0042742: defense response to bacterium2.22E-02
136GO:0009831: plant-type cell wall modification involved in multidimensional cell growth2.35E-02
137GO:0009561: megagametogenesis2.49E-02
138GO:0009306: protein secretion2.49E-02
139GO:0080022: primary root development2.79E-02
140GO:0034220: ion transmembrane transport2.79E-02
141GO:0006662: glycerol ether metabolic process2.94E-02
142GO:0046323: glucose import2.94E-02
143GO:0015986: ATP synthesis coupled proton transport3.10E-02
144GO:0000302: response to reactive oxygen species3.42E-02
145GO:0042744: hydrogen peroxide catabolic process3.55E-02
146GO:0032502: developmental process3.58E-02
147GO:0009790: embryo development3.63E-02
148GO:0030163: protein catabolic process3.75E-02
149GO:0009567: double fertilization forming a zygote and endosperm3.92E-02
150GO:0009828: plant-type cell wall loosening3.92E-02
151GO:0016126: sterol biosynthetic process4.44E-02
RankGO TermAdjusted P value
1GO:0005048: signal sequence binding0.00E+00
2GO:0033728: divinyl chlorophyllide a 8-vinyl-reductase activity0.00E+00
3GO:0046406: magnesium protoporphyrin IX methyltransferase activity0.00E+00
4GO:0047513: 1,2-alpha-L-fucosidase activity0.00E+00
5GO:0050515: 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity0.00E+00
6GO:0051744: 3,8-divinyl protochlorophyllide a 8-vinyl reductase activity0.00E+00
7GO:0046428: 1,4-dihydroxy-2-naphthoate octaprenyltransferase activity0.00E+00
8GO:0008887: glycerate kinase activity0.00E+00
9GO:0004852: uroporphyrinogen-III synthase activity0.00E+00
10GO:0019843: rRNA binding2.71E-24
11GO:0003735: structural constituent of ribosome4.42E-17
12GO:0003755: peptidyl-prolyl cis-trans isomerase activity1.46E-07
13GO:0016851: magnesium chelatase activity2.04E-07
14GO:0005528: FK506 binding5.86E-06
15GO:0043023: ribosomal large subunit binding4.07E-05
16GO:0008266: poly(U) RNA binding8.72E-05
17GO:0004801: sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity3.40E-04
18GO:0004425: indole-3-glycerol-phosphate synthase activity3.40E-04
19GO:0050567: glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity3.40E-04
20GO:0008124: 4-alpha-hydroxytetrahydrobiopterin dehydratase activity3.40E-04
21GO:0004163: diphosphomevalonate decarboxylase activity3.40E-04
22GO:0042286: glutamate-1-semialdehyde 2,1-aminomutase activity3.40E-04
23GO:0008047: enzyme activator activity7.37E-04
24GO:0000774: adenyl-nucleotide exchange factor activity7.40E-04
25GO:0016630: protochlorophyllide reductase activity7.40E-04
26GO:0019171: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity7.40E-04
27GO:0047100: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity7.40E-04
28GO:0051082: unfolded protein binding8.42E-04
29GO:0016168: chlorophyll binding8.43E-04
30GO:0031072: heat shock protein binding1.10E-03
31GO:0050734: hydroxycinnamoyltransferase activity1.20E-03
32GO:0004751: ribose-5-phosphate isomerase activity1.20E-03
33GO:0016620: oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor1.20E-03
34GO:0080054: low-affinity nitrate transmembrane transporter activity1.20E-03
35GO:0016787: hydrolase activity1.66E-03
36GO:0016149: translation release factor activity, codon specific1.72E-03
37GO:0004550: nucleoside diphosphate kinase activity1.72E-03
38GO:0008097: 5S rRNA binding1.72E-03
39GO:0051087: chaperone binding1.88E-03
40GO:0004845: uracil phosphoribosyltransferase activity2.31E-03
41GO:0004345: glucose-6-phosphate dehydrogenase activity2.31E-03
42GO:0016836: hydro-lyase activity2.31E-03
43GO:0004045: aminoacyl-tRNA hydrolase activity2.31E-03
44GO:0016987: sigma factor activity2.31E-03
45GO:0010328: auxin influx transmembrane transporter activity2.31E-03
46GO:0043495: protein anchor2.31E-03
47GO:0004392: heme oxygenase (decyclizing) activity2.31E-03
48GO:0003841: 1-acylglycerol-3-phosphate O-acyltransferase activity2.31E-03
49GO:0004659: prenyltransferase activity2.31E-03
50GO:0001053: plastid sigma factor activity2.31E-03
51GO:0030570: pectate lyase activity2.46E-03
52GO:0042802: identical protein binding2.77E-03
53GO:0003959: NADPH dehydrogenase activity2.96E-03
54GO:0004791: thioredoxin-disulfide reductase activity3.63E-03
55GO:0004130: cytochrome-c peroxidase activity3.65E-03
56GO:0004366: glycerol-3-phosphate O-acyltransferase activity3.65E-03
57GO:0016688: L-ascorbate peroxidase activity3.65E-03
58GO:0090447: glycerol-3-phosphate 2-O-acyltransferase activity3.65E-03
59GO:0003723: RNA binding3.99E-03
60GO:0004124: cysteine synthase activity4.40E-03
61GO:0051920: peroxiredoxin activity4.40E-03
62GO:0033743: peptide-methionine (R)-S-oxide reductase activity4.40E-03
63GO:0004849: uridine kinase activity4.40E-03
64GO:0016671: oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor4.74E-03
65GO:0005525: GTP binding4.96E-03
66GO:0019899: enzyme binding5.19E-03
67GO:0004620: phospholipase activity5.19E-03
68GO:0003729: mRNA binding5.69E-03
69GO:0016209: antioxidant activity6.03E-03
70GO:0008312: 7S RNA binding6.03E-03
71GO:0052747: sinapyl alcohol dehydrogenase activity6.03E-03
72GO:0004033: aldo-keto reductase (NADP) activity6.03E-03
73GO:0008236: serine-type peptidase activity7.48E-03
74GO:0003747: translation release factor activity7.85E-03
75GO:0015450: P-P-bond-hydrolysis-driven protein transmembrane transporter activity7.88E-03
76GO:0050661: NADP binding1.14E-02
77GO:0008378: galactosyltransferase activity1.20E-02
78GO:0045551: cinnamyl-alcohol dehydrogenase activity1.20E-02
79GO:0009982: pseudouridine synthase activity1.31E-02
80GO:0004565: beta-galactosidase activity1.31E-02
81GO:0004022: alcohol dehydrogenase (NAD) activity1.31E-02
82GO:0016788: hydrolase activity, acting on ester bonds1.67E-02
83GO:0031409: pigment binding1.67E-02
84GO:0005509: calcium ion binding1.94E-02
85GO:0022891: substrate-specific transmembrane transporter activity2.35E-02
86GO:0003756: protein disulfide isomerase activity2.49E-02
87GO:0016746: transferase activity, transferring acyl groups2.56E-02
88GO:0047134: protein-disulfide reductase activity2.64E-02
89GO:0042803: protein homodimerization activity2.85E-02
90GO:0008080: N-acetyltransferase activity2.94E-02
91GO:0046933: proton-transporting ATP synthase activity, rotational mechanism2.94E-02
92GO:0016740: transferase activity2.99E-02
93GO:0005355: glucose transmembrane transporter activity3.10E-02
94GO:0050662: coenzyme binding3.10E-02
95GO:0016829: lyase activity3.37E-02
96GO:0030170: pyridoxal phosphate binding3.46E-02
97GO:0051015: actin filament binding3.75E-02
98GO:0016791: phosphatase activity3.92E-02
99GO:0008483: transaminase activity4.09E-02
100GO:0015250: water channel activity4.44E-02
RankGO TermAdjusted P value
1GO:0098572: stromal side of plastid thylakoid membrane0.00E+00
2GO:0044391: ribosomal subunit0.00E+00
3GO:0009515: granal stacked thylakoid0.00E+00
4GO:0009507: chloroplast1.23E-84
5GO:0009570: chloroplast stroma1.75E-69
6GO:0009941: chloroplast envelope2.17E-55
7GO:0009535: chloroplast thylakoid membrane2.22E-38
8GO:0009579: thylakoid3.25E-36
9GO:0009534: chloroplast thylakoid1.26E-34
10GO:0009543: chloroplast thylakoid lumen1.34E-22
11GO:0031977: thylakoid lumen2.88E-19
12GO:0005840: ribosome4.54E-19
13GO:0030095: chloroplast photosystem II6.65E-10
14GO:0010007: magnesium chelatase complex4.22E-08
15GO:0009654: photosystem II oxygen evolving complex1.77E-07
16GO:0019898: extrinsic component of membrane1.41E-06
17GO:0016020: membrane1.21E-05
18GO:0031969: chloroplast membrane4.26E-05
19GO:0009533: chloroplast stromal thylakoid2.89E-04
20GO:0043674: columella3.40E-04
21GO:0030956: glutamyl-tRNA(Gln) amidotransferase complex3.40E-04
22GO:0009547: plastid ribosome3.40E-04
23GO:0009523: photosystem II4.50E-04
24GO:0010598: NAD(P)H dehydrogenase complex (plastoquinone)5.35E-04
25GO:0080085: signal recognition particle, chloroplast targeting7.40E-04
26GO:0032040: small-subunit processome9.69E-04
27GO:0000311: plastid large ribosomal subunit9.69E-04
28GO:0010287: plastoglobule1.09E-03
29GO:0009509: chromoplast1.20E-03
30GO:0000312: plastid small ribosomal subunit1.23E-03
31GO:0032432: actin filament bundle1.72E-03
32GO:0042651: thylakoid membrane1.88E-03
33GO:0015935: small ribosomal subunit2.06E-03
34GO:0009526: plastid envelope2.31E-03
35GO:0055035: plastid thylakoid membrane2.96E-03
36GO:0009522: photosystem I3.63E-03
37GO:0045261: proton-transporting ATP synthase complex, catalytic core F(1)3.65E-03
38GO:0009536: plastid3.75E-03
39GO:0042807: central vacuole5.19E-03
40GO:0010319: stromule5.37E-03
41GO:0022625: cytosolic large ribosomal subunit5.62E-03
42GO:0030529: intracellular ribonucleoprotein complex6.03E-03
43GO:0048046: apoplast6.43E-03
44GO:0005786: signal recognition particle, endoplasmic reticulum targeting6.92E-03
45GO:0008180: COP9 signalosome7.85E-03
46GO:0042644: chloroplast nucleoid7.85E-03
47GO:0015934: large ribosomal subunit9.11E-03
48GO:0005884: actin filament1.09E-02
49GO:0009508: plastid chromosome1.31E-02
50GO:0030076: light-harvesting complex1.55E-02
51GO:0043234: protein complex1.67E-02
52GO:0009706: chloroplast inner membrane2.49E-02
53GO:0005759: mitochondrial matrix3.91E-02
54GO:0009295: nucleoid4.09E-02
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Gene type



Gene DE type