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

AT4G29060

GO-BP
GO-MF
GO-CC
RankGO TermAdjusted P value
1GO:0010323: negative regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway0.00E+00
2GO:0032194: ubiquinone biosynthetic process via 3,4-dihydroxy-5-polyprenylbenzoate0.00E+00
3GO:0090071: negative regulation of ribosome biogenesis0.00E+00
4GO:0015742: alpha-ketoglutarate transport0.00E+00
5GO:0042407: cristae formation0.00E+00
6GO:0042821: pyridoxal biosynthetic process0.00E+00
7GO:0016553: base conversion or substitution editing0.00E+00
8GO:0060416: response to growth hormone0.00E+00
9GO:0015882: L-ascorbic acid transport0.00E+00
10GO:0042820: vitamin B6 catabolic process0.00E+00
11GO:0006399: tRNA metabolic process0.00E+00
12GO:0018160: peptidyl-pyrromethane cofactor linkage0.00E+00
13GO:0032544: plastid translation1.52E-14
14GO:0015995: chlorophyll biosynthetic process6.56E-11
15GO:0009658: chloroplast organization1.30E-10
16GO:0006412: translation1.47E-09
17GO:0006782: protoporphyrinogen IX biosynthetic process4.08E-09
18GO:0006783: heme biosynthetic process1.69E-07
19GO:1901259: chloroplast rRNA processing2.59E-06
20GO:0010275: NAD(P)H dehydrogenase complex assembly3.47E-06
21GO:0042254: ribosome biogenesis8.94E-06
22GO:0006779: porphyrin-containing compound biosynthetic process1.72E-05
23GO:0009089: lysine biosynthetic process via diaminopimelate2.89E-05
24GO:0010027: thylakoid membrane organization4.51E-05
25GO:0045038: protein import into chloroplast thylakoid membrane8.02E-05
26GO:0006655: phosphatidylglycerol biosynthetic process1.17E-04
27GO:0015979: photosynthesis1.76E-04
28GO:0009306: protein secretion1.78E-04
29GO:0008033: tRNA processing2.23E-04
30GO:0042255: ribosome assembly2.66E-04
31GO:0006353: DNA-templated transcription, termination2.66E-04
32GO:0006438: valyl-tRNA aminoacylation2.75E-04
33GO:0009443: pyridoxal 5'-phosphate salvage2.75E-04
34GO:0009090: homoserine biosynthetic process2.75E-04
35GO:0043489: RNA stabilization2.75E-04
36GO:0097056: selenocysteinyl-tRNA(Sec) biosynthetic process2.75E-04
37GO:1904966: positive regulation of vitamin E biosynthetic process2.75E-04
38GO:0006426: glycyl-tRNA aminoacylation2.75E-04
39GO:1904964: positive regulation of phytol biosynthetic process2.75E-04
40GO:0042371: vitamin K biosynthetic process2.75E-04
41GO:0006436: tryptophanyl-tRNA aminoacylation2.75E-04
42GO:1902458: positive regulation of stomatal opening2.75E-04
43GO:0010028: xanthophyll cycle2.75E-04
44GO:0034337: RNA folding2.75E-04
45GO:0006434: seryl-tRNA aminoacylation2.75E-04
46GO:0009793: embryo development ending in seed dormancy2.89E-04
47GO:0071482: cellular response to light stimulus3.27E-04
48GO:1902326: positive regulation of chlorophyll biosynthetic process6.04E-04
49GO:1900871: chloroplast mRNA modification6.04E-04
50GO:0006423: cysteinyl-tRNA aminoacylation6.04E-04
51GO:0080148: negative regulation of response to water deprivation6.04E-04
52GO:1903426: regulation of reactive oxygen species biosynthetic process6.04E-04
53GO:0043039: tRNA aminoacylation6.04E-04
54GO:0043085: positive regulation of catalytic activity6.30E-04
55GO:0006352: DNA-templated transcription, initiation6.30E-04
56GO:0016024: CDP-diacylglycerol biosynthetic process7.20E-04
57GO:0010020: chloroplast fission9.17E-04
58GO:0009790: embryo development9.32E-04
59GO:0010581: regulation of starch biosynthetic process9.79E-04
60GO:0006954: inflammatory response9.79E-04
61GO:0090391: granum assembly9.79E-04
62GO:0006518: peptide metabolic process9.79E-04
63GO:0006617: SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition9.79E-04
64GO:0090351: seedling development1.02E-03
65GO:0006636: unsaturated fatty acid biosynthetic process1.14E-03
66GO:0006418: tRNA aminoacylation for protein translation1.38E-03
67GO:0015729: oxaloacetate transport1.40E-03
68GO:0010239: chloroplast mRNA processing1.40E-03
69GO:0006241: CTP biosynthetic process1.40E-03
70GO:0006165: nucleoside diphosphate phosphorylation1.40E-03
71GO:0006228: UTP biosynthetic process1.40E-03
72GO:0016556: mRNA modification1.40E-03
73GO:0080158: chloroplast ribulose bisphosphate carboxylase complex biogenesis1.40E-03
74GO:2001141: regulation of RNA biosynthetic process1.40E-03
75GO:0009067: aspartate family amino acid biosynthetic process1.40E-03
76GO:0051085: chaperone mediated protein folding requiring cofactor1.40E-03
77GO:0007005: mitochondrion organization1.66E-03
78GO:0006183: GTP biosynthetic process1.87E-03
79GO:0006221: pyrimidine nucleotide biosynthetic process1.87E-03
80GO:0006749: glutathione metabolic process1.87E-03
81GO:0071483: cellular response to blue light1.87E-03
82GO:0044205: 'de novo' UMP biosynthetic process1.87E-03
83GO:0006808: regulation of nitrogen utilization1.87E-03
84GO:0019676: ammonia assimilation cycle1.87E-03
85GO:0015743: malate transport1.87E-03
86GO:0006364: rRNA processing2.00E-03
87GO:0009409: response to cold2.33E-03
88GO:0009247: glycolipid biosynthetic process2.39E-03
89GO:0071423: malate transmembrane transport2.39E-03
90GO:0016120: carotene biosynthetic process2.39E-03
91GO:0010236: plastoquinone biosynthetic process2.39E-03
92GO:0016123: xanthophyll biosynthetic process2.39E-03
93GO:0032973: amino acid export2.95E-03
94GO:0032502: developmental process3.26E-03
95GO:0042026: protein refolding3.55E-03
96GO:0042372: phylloquinone biosynthetic process3.55E-03
97GO:0017148: negative regulation of translation3.55E-03
98GO:0009088: threonine biosynthetic process3.55E-03
99GO:0010019: chloroplast-nucleus signaling pathway3.55E-03
100GO:0009955: adaxial/abaxial pattern specification3.55E-03
101GO:0006614: SRP-dependent cotranslational protein targeting to membrane4.19E-03
102GO:0006207: 'de novo' pyrimidine nucleobase biosynthetic process4.19E-03
103GO:0006401: RNA catabolic process4.19E-03
104GO:0045995: regulation of embryonic development4.19E-03
105GO:0009395: phospholipid catabolic process4.19E-03
106GO:0009772: photosynthetic electron transport in photosystem II4.19E-03
107GO:0043090: amino acid import4.19E-03
108GO:0048564: photosystem I assembly4.86E-03
109GO:0006402: mRNA catabolic process4.86E-03
110GO:0006605: protein targeting4.86E-03
111GO:0019375: galactolipid biosynthetic process4.86E-03
112GO:0009704: de-etiolation4.86E-03
113GO:2000070: regulation of response to water deprivation4.86E-03
114GO:0052543: callose deposition in cell wall4.86E-03
115GO:0022900: electron transport chain5.57E-03
116GO:0019430: removal of superoxide radicals5.57E-03
117GO:0009657: plastid organization5.57E-03
118GO:0017004: cytochrome complex assembly5.57E-03
119GO:0048481: plant ovule development5.76E-03
120GO:0080144: amino acid homeostasis6.31E-03
121GO:0098656: anion transmembrane transport6.31E-03
122GO:0055114: oxidation-reduction process6.34E-03
123GO:0009451: RNA modification6.47E-03
124GO:0010205: photoinhibition7.09E-03
125GO:0043067: regulation of programmed cell death7.09E-03
126GO:0009086: methionine biosynthetic process7.09E-03
127GO:0010380: regulation of chlorophyll biosynthetic process7.09E-03
128GO:0031425: chloroplast RNA processing7.09E-03
129GO:0045036: protein targeting to chloroplast7.90E-03
130GO:0009773: photosynthetic electron transport in photosystem I8.74E-03
131GO:0019684: photosynthesis, light reaction8.74E-03
132GO:0009073: aromatic amino acid family biosynthetic process8.74E-03
133GO:0006415: translational termination8.74E-03
134GO:0045037: protein import into chloroplast stroma9.61E-03
135GO:0010628: positive regulation of gene expression1.05E-02
136GO:0009691: cytokinin biosynthetic process1.05E-02
137GO:0006006: glucose metabolic process1.05E-02
138GO:0019253: reductive pentose-phosphate cycle1.14E-02
139GO:0000027: ribosomal large subunit assembly1.44E-02
140GO:0031408: oxylipin biosynthetic process1.65E-02
141GO:0016226: iron-sulfur cluster assembly1.76E-02
142GO:0006730: one-carbon metabolic process1.76E-02
143GO:0045454: cell redox homeostasis1.81E-02
144GO:0009411: response to UV1.88E-02
145GO:0016117: carotenoid biosynthetic process2.11E-02
146GO:0006662: glycerol ether metabolic process2.35E-02
147GO:0010197: polar nucleus fusion2.35E-02
148GO:0009741: response to brassinosteroid2.35E-02
149GO:0006814: sodium ion transport2.47E-02
150GO:0008654: phospholipid biosynthetic process2.60E-02
151GO:0006413: translational initiation2.93E-02
152GO:0040008: regulation of growth3.00E-02
153GO:0008380: RNA splicing3.75E-02
154GO:0009627: systemic acquired resistance3.84E-02
155GO:0042742: defense response to bacterium3.95E-02
156GO:0018298: protein-chromophore linkage4.29E-02
157GO:0008219: cell death4.29E-02
158GO:0009735: response to cytokinin4.30E-02
159GO:0006499: N-terminal protein myristoylation4.59E-02
160GO:0009407: toxin catabolic process4.59E-02
161GO:0048527: lateral root development4.75E-02
162GO:0009631: cold acclimation4.75E-02
163GO:0009416: response to light stimulus4.79E-02
RankGO TermAdjusted P value
1GO:0050236: pyridoxine:NADP 4-dehydrogenase activity0.00E+00
2GO:0000979: RNA polymerase II core promoter sequence-specific DNA binding0.00E+00
3GO:0046428: 1,4-dihydroxy-2-naphthoate octaprenyltransferase activity0.00E+00
4GO:0009979: 16:0 monogalactosyldiacylglycerol desaturase activity0.00E+00
5GO:0004853: uroporphyrinogen decarboxylase activity0.00E+00
6GO:0004151: dihydroorotase activity0.00E+00
7GO:0004418: hydroxymethylbilane synthase activity0.00E+00
8GO:0015229: L-ascorbic acid transporter activity0.00E+00
9GO:0015038: glutathione disulfide oxidoreductase activity0.00E+00
10GO:0015139: alpha-ketoglutarate transmembrane transporter activity0.00E+00
11GO:0005048: signal sequence binding0.00E+00
12GO:0009974: zeinoxanthin epsilon hydroxylase activity0.00E+00
13GO:0019843: rRNA binding2.17E-20
14GO:0003735: structural constituent of ribosome3.81E-11
15GO:0008839: 4-hydroxy-tetrahydrodipicolinate reductase3.47E-06
16GO:0070402: NADPH binding1.24E-05
17GO:0003723: RNA binding2.07E-05
18GO:0016987: sigma factor activity5.05E-05
19GO:0001053: plastid sigma factor activity5.05E-05
20GO:0050567: glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity2.75E-04
21GO:0004828: serine-tRNA ligase activity2.75E-04
22GO:0004655: porphobilinogen synthase activity2.75E-04
23GO:0052381: tRNA dimethylallyltransferase activity2.75E-04
24GO:0004832: valine-tRNA ligase activity2.75E-04
25GO:0004830: tryptophan-tRNA ligase activity2.75E-04
26GO:0004820: glycine-tRNA ligase activity2.75E-04
27GO:0004654: polyribonucleotide nucleotidyltransferase activity2.75E-04
28GO:0042286: glutamate-1-semialdehyde 2,1-aminomutase activity2.75E-04
29GO:0016717: oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water3.27E-04
30GO:0008047: enzyme activator activity5.46E-04
31GO:0004817: cysteine-tRNA ligase activity6.04E-04
32GO:0004412: homoserine dehydrogenase activity6.04E-04
33GO:0016630: protochlorophyllide reductase activity6.04E-04
34GO:0015367: oxoglutarate:malate antiporter activity6.04E-04
35GO:0047100: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity6.04E-04
36GO:0042389: omega-3 fatty acid desaturase activity6.04E-04
37GO:0004326: tetrahydrofolylpolyglutamate synthase activity6.04E-04
38GO:0009977: proton motive force dependent protein transmembrane transporter activity6.04E-04
39GO:0046509: 1,2-diacylglycerol 3-beta-galactosyltransferase activity6.04E-04
40GO:0008266: poly(U) RNA binding9.17E-04
41GO:0017150: tRNA dihydrouridine synthase activity9.79E-04
42GO:0004148: dihydrolipoyl dehydrogenase activity9.79E-04
43GO:0004072: aspartate kinase activity1.40E-03
44GO:0015131: oxaloacetate transmembrane transporter activity1.40E-03
45GO:0035250: UDP-galactosyltransferase activity1.40E-03
46GO:0016149: translation release factor activity, codon specific1.40E-03
47GO:0016851: magnesium chelatase activity1.40E-03
48GO:0004550: nucleoside diphosphate kinase activity1.40E-03
49GO:0043023: ribosomal large subunit binding1.40E-03
50GO:0008097: 5S rRNA binding1.40E-03
51GO:0004365: glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity1.40E-03
52GO:0001872: (1->3)-beta-D-glucan binding1.40E-03
53GO:0004176: ATP-dependent peptidase activity1.52E-03
54GO:0043495: protein anchor1.87E-03
55GO:0003841: 1-acylglycerol-3-phosphate O-acyltransferase activity1.87E-03
56GO:0004659: prenyltransferase activity1.87E-03
57GO:0003727: single-stranded RNA binding1.97E-03
58GO:0004812: aminoacyl-tRNA ligase activity2.13E-03
59GO:0016773: phosphotransferase activity, alcohol group as acceptor2.39E-03
60GO:0003959: NADPH dehydrogenase activity2.39E-03
61GO:0004040: amidase activity2.39E-03
62GO:0004791: thioredoxin-disulfide reductase activity2.67E-03
63GO:0003729: mRNA binding2.87E-03
64GO:0004605: phosphatidate cytidylyltransferase activity2.95E-03
65GO:0016671: oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor3.48E-03
66GO:0008237: metallopeptidase activity3.93E-03
67GO:0016831: carboxy-lyase activity4.19E-03
68GO:0015140: malate transmembrane transporter activity4.19E-03
69GO:0019899: enzyme binding4.19E-03
70GO:0008312: 7S RNA binding4.86E-03
71GO:0004033: aldo-keto reductase (NADP) activity4.86E-03
72GO:0015450: P-P-bond-hydrolysis-driven protein transmembrane transporter activity5.76E-03
73GO:0003924: GTPase activity5.84E-03
74GO:0003747: translation release factor activity6.31E-03
75GO:0004222: metalloendopeptidase activity6.35E-03
76GO:0016491: oxidoreductase activity6.89E-03
77GO:0050661: NADP binding8.33E-03
78GO:0042802: identical protein binding8.53E-03
79GO:0044183: protein binding involved in protein folding8.74E-03
80GO:0005525: GTP binding9.04E-03
81GO:0051537: 2 iron, 2 sulfur cluster binding1.02E-02
82GO:0000175: 3'-5'-exoribonuclease activity1.05E-02
83GO:0005315: inorganic phosphate transmembrane transporter activity1.05E-02
84GO:0031072: heat shock protein binding1.05E-02
85GO:0003755: peptidyl-prolyl cis-trans isomerase activity1.10E-02
86GO:0016887: ATPase activity1.14E-02
87GO:0042973: glucan endo-1,3-beta-D-glucosidase activity1.14E-02
88GO:0003899: DNA-directed 5'-3' RNA polymerase activity1.27E-02
89GO:0003690: double-stranded DNA binding1.32E-02
90GO:0051536: iron-sulfur cluster binding1.44E-02
91GO:0051082: unfolded protein binding1.82E-02
92GO:0015035: protein disulfide oxidoreductase activity1.87E-02
93GO:0022891: substrate-specific transmembrane transporter activity1.88E-02
94GO:0008514: organic anion transmembrane transporter activity1.99E-02
95GO:0047134: protein-disulfide reductase activity2.11E-02
96GO:0008080: N-acetyltransferase activity2.35E-02
97GO:0010181: FMN binding2.47E-02
98GO:0009055: electron carrier activity2.58E-02
99GO:0004519: endonuclease activity2.62E-02
100GO:0008565: protein transporter activity2.73E-02
101GO:0008483: transaminase activity3.27E-02
102GO:0016597: amino acid binding3.41E-02
103GO:0003743: translation initiation factor activity3.67E-02
104GO:0016168: chlorophyll binding3.69E-02
105GO:0030247: polysaccharide binding3.99E-02
106GO:0003824: catalytic activity4.51E-02
107GO:0000287: magnesium ion binding4.75E-02
RankGO TermAdjusted P value
1GO:0044391: ribosomal subunit0.00E+00
2GO:0009507: chloroplast2.93E-91
3GO:0009570: chloroplast stroma2.51E-54
4GO:0009941: chloroplast envelope4.39E-40
5GO:0009535: chloroplast thylakoid membrane1.38E-21
6GO:0005840: ribosome1.48E-14
7GO:0009579: thylakoid2.82E-14
8GO:0009536: plastid1.07E-09
9GO:0009706: chloroplast inner membrane2.92E-07
10GO:0009543: chloroplast thylakoid lumen6.47E-07
11GO:0009295: nucleoid1.50E-06
12GO:0031969: chloroplast membrane1.53E-06
13GO:0033281: TAT protein transport complex1.24E-05
14GO:0009534: chloroplast thylakoid1.30E-05
15GO:0000311: plastid large ribosomal subunit3.63E-05
16GO:0009654: photosystem II oxygen evolving complex1.06E-04
17GO:0042651: thylakoid membrane1.06E-04
18GO:0030956: glutamyl-tRNA(Gln) amidotransferase complex2.75E-04
19GO:0009547: plastid ribosome2.75E-04
20GO:0042170: plastid membrane6.04E-04
21GO:0080085: signal recognition particle, chloroplast targeting6.04E-04
22GO:0009508: plastid chromosome8.15E-04
23GO:0015934: large ribosomal subunit8.93E-04
24GO:0031977: thylakoid lumen1.24E-03
25GO:0042646: plastid nucleoid1.40E-03
26GO:0019898: extrinsic component of membrane2.86E-03
27GO:0016363: nuclear matrix3.55E-03
28GO:0010319: stromule3.93E-03
29GO:0009539: photosystem II reaction center5.57E-03
30GO:0005786: signal recognition particle, endoplasmic reticulum targeting5.57E-03
31GO:0009707: chloroplast outer membrane5.76E-03
32GO:0010598: NAD(P)H dehydrogenase complex (plastoquinone)6.31E-03
33GO:0005763: mitochondrial small ribosomal subunit6.31E-03
34GO:0032040: small-subunit processome9.61E-03
35GO:0030095: chloroplast photosystem II1.14E-02
36GO:0000312: plastid small ribosomal subunit1.14E-02
37GO:0022626: cytosolic ribosome1.30E-02
38GO:0015935: small ribosomal subunit1.65E-02
39GO:0009532: plastid stroma1.65E-02
40GO:0005623: cell2.34E-02
41GO:0009523: photosystem II2.60E-02
42GO:0030529: intracellular ribonucleoprotein complex3.55E-02
43GO:0046658: anchored component of plasma membrane4.15E-02
44GO:0016020: membrane4.16E-02
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Gene type



Gene DE type