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

AT3G04260

GO-BP
GO-MF
GO-CC
RankGO TermAdjusted P value
1GO:0032194: ubiquinone biosynthetic process via 3,4-dihydroxy-5-polyprenylbenzoate0.00E+00
2GO:0070681: glutaminyl-tRNAGln biosynthesis via transamidation0.00E+00
3GO:0002949: tRNA threonylcarbamoyladenosine modification0.00E+00
4GO:0016553: base conversion or substitution editing0.00E+00
5GO:0060416: response to growth hormone0.00E+00
6GO:0018023: peptidyl-lysine trimethylation0.00E+00
7GO:0000372: Group I intron splicing0.00E+00
8GO:0006399: tRNA metabolic process0.00E+00
9GO:0070125: mitochondrial translational elongation0.00E+00
10GO:0006429: leucyl-tRNA aminoacylation0.00E+00
11GO:0010275: NAD(P)H dehydrogenase complex assembly0.00E+00
12GO:0002184: cytoplasmic translational termination0.00E+00
13GO:0010323: negative regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway0.00E+00
14GO:0006412: translation3.77E-12
15GO:0032544: plastid translation1.44E-11
16GO:0042254: ribosome biogenesis2.60E-07
17GO:0015995: chlorophyll biosynthetic process3.62E-07
18GO:0016123: xanthophyll biosynthetic process1.53E-06
19GO:0009658: chloroplast organization2.93E-06
20GO:0009793: embryo development ending in seed dormancy4.72E-06
21GO:1901259: chloroplast rRNA processing5.09E-06
22GO:0010027: thylakoid membrane organization5.57E-06
23GO:0016120: carotene biosynthetic process1.23E-04
24GO:0032543: mitochondrial translation1.23E-04
25GO:0045038: protein import into chloroplast thylakoid membrane1.23E-04
26GO:0006655: phosphatidylglycerol biosynthetic process1.78E-04
27GO:0042372: phylloquinone biosynthetic process2.41E-04
28GO:0009306: protein secretion3.02E-04
29GO:0009790: embryo development3.20E-04
30GO:0016117: carotenoid biosynthetic process3.36E-04
31GO:0006438: valyl-tRNA aminoacylation3.57E-04
32GO:0000476: maturation of 4.5S rRNA3.57E-04
33GO:0000967: rRNA 5'-end processing3.57E-04
34GO:1903409: reactive oxygen species biosynthetic process3.57E-04
35GO:0043489: RNA stabilization3.57E-04
36GO:0097056: selenocysteinyl-tRNA(Sec) biosynthetic process3.57E-04
37GO:1904966: positive regulation of vitamin E biosynthetic process3.57E-04
38GO:0006426: glycyl-tRNA aminoacylation3.57E-04
39GO:1904964: positive regulation of phytol biosynthetic process3.57E-04
40GO:0042371: vitamin K biosynthetic process3.57E-04
41GO:1902458: positive regulation of stomatal opening3.57E-04
42GO:0034337: RNA folding3.57E-04
43GO:0010729: positive regulation of hydrogen peroxide biosynthetic process3.57E-04
44GO:0006434: seryl-tRNA aminoacylation3.57E-04
45GO:0006353: DNA-templated transcription, termination3.92E-04
46GO:0015979: photosynthesis4.12E-04
47GO:0010206: photosystem II repair5.76E-04
48GO:1902326: positive regulation of chlorophyll biosynthetic process7.77E-04
49GO:0018026: peptidyl-lysine monomethylation7.77E-04
50GO:0080148: negative regulation of response to water deprivation7.77E-04
51GO:1903426: regulation of reactive oxygen species biosynthetic process7.77E-04
52GO:0034470: ncRNA processing7.77E-04
53GO:0043039: tRNA aminoacylation7.77E-04
54GO:0009773: photosynthetic electron transport in photosystem I9.13E-04
55GO:0019684: photosynthesis, light reaction9.13E-04
56GO:0006415: translational termination9.13E-04
57GO:0016024: CDP-diacylglycerol biosynthetic process1.04E-03
58GO:0006954: inflammatory response1.26E-03
59GO:0006518: peptide metabolic process1.26E-03
60GO:0006617: SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition1.26E-03
61GO:0009226: nucleotide-sugar biosynthetic process1.81E-03
62GO:0006424: glutamyl-tRNA aminoacylation1.81E-03
63GO:0016556: mRNA modification1.81E-03
64GO:0046739: transport of virus in multicellular host1.81E-03
65GO:2001141: regulation of RNA biosynthetic process1.81E-03
66GO:0010239: chloroplast mRNA processing1.81E-03
67GO:0006418: tRNA aminoacylation for protein translation2.03E-03
68GO:0009451: RNA modification2.24E-03
69GO:0006749: glutathione metabolic process2.44E-03
70GO:0006808: regulation of nitrogen utilization2.44E-03
71GO:0009765: photosynthesis, light harvesting2.44E-03
72GO:0009247: glycolipid biosynthetic process3.11E-03
73GO:0000304: response to singlet oxygen3.11E-03
74GO:0006564: L-serine biosynthetic process3.11E-03
75GO:0010236: plastoquinone biosynthetic process3.11E-03
76GO:0008033: tRNA processing3.38E-03
77GO:0000413: protein peptidyl-prolyl isomerization3.38E-03
78GO:0016554: cytidine to uridine editing3.85E-03
79GO:0032973: amino acid export3.85E-03
80GO:0018258: protein O-linked glycosylation via hydroxyproline3.85E-03
81GO:0010190: cytochrome b6f complex assembly3.85E-03
82GO:0010405: arabinogalactan protein metabolic process3.85E-03
83GO:0042026: protein refolding4.64E-03
84GO:0000462: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)4.64E-03
85GO:0006458: 'de novo' protein folding4.64E-03
86GO:0010019: chloroplast-nucleus signaling pathway4.64E-03
87GO:0009955: adaxial/abaxial pattern specification4.64E-03
88GO:0006614: SRP-dependent cotranslational protein targeting to membrane5.48E-03
89GO:0006821: chloride transport5.48E-03
90GO:0006400: tRNA modification5.48E-03
91GO:0006401: RNA catabolic process5.48E-03
92GO:0045995: regulation of embryonic development5.48E-03
93GO:0009395: phospholipid catabolic process5.48E-03
94GO:0009772: photosynthetic electron transport in photosystem II5.48E-03
95GO:0043090: amino acid import5.48E-03
96GO:0007169: transmembrane receptor protein tyrosine kinase signaling pathway6.16E-03
97GO:0006402: mRNA catabolic process6.37E-03
98GO:0042255: ribosome assembly6.37E-03
99GO:0006605: protein targeting6.37E-03
100GO:0019375: galactolipid biosynthetic process6.37E-03
101GO:0009704: de-etiolation6.37E-03
102GO:2000070: regulation of response to water deprivation6.37E-03
103GO:0016559: peroxisome fission6.37E-03
104GO:0048564: photosystem I assembly6.37E-03
105GO:0010497: plasmodesmata-mediated intercellular transport7.30E-03
106GO:0009657: plastid organization7.30E-03
107GO:0017004: cytochrome complex assembly7.30E-03
108GO:0071482: cellular response to light stimulus7.30E-03
109GO:0080144: amino acid homeostasis8.29E-03
110GO:0006783: heme biosynthetic process8.29E-03
111GO:0000373: Group II intron splicing8.29E-03
112GO:0009051: pentose-phosphate shunt, oxidative branch8.29E-03
113GO:0018298: protein-chromophore linkage8.51E-03
114GO:1900865: chloroplast RNA modification9.31E-03
115GO:0031425: chloroplast RNA processing9.31E-03
116GO:0010205: photoinhibition9.31E-03
117GO:0009407: toxin catabolic process9.39E-03
118GO:0006782: protoporphyrinogen IX biosynthetic process1.04E-02
119GO:0006397: mRNA processing1.13E-02
120GO:0009089: lysine biosynthetic process via diaminopimelate1.15E-02
121GO:0009073: aromatic amino acid family biosynthetic process1.15E-02
122GO:0006352: DNA-templated transcription, initiation1.15E-02
123GO:0018119: peptidyl-cysteine S-nitrosylation1.15E-02
124GO:0006457: protein folding1.18E-02
125GO:0045037: protein import into chloroplast stroma1.27E-02
126GO:0010628: positive regulation of gene expression1.39E-02
127GO:0006006: glucose metabolic process1.39E-02
128GO:0009767: photosynthetic electron transport chain1.39E-02
129GO:0010020: chloroplast fission1.51E-02
130GO:0048768: root hair cell tip growth1.51E-02
131GO:0009636: response to toxic substance1.57E-02
132GO:0090351: seedling development1.64E-02
133GO:0006636: unsaturated fatty acid biosynthetic process1.77E-02
134GO:0000027: ribosomal large subunit assembly1.90E-02
135GO:0061077: chaperone-mediated protein folding2.18E-02
136GO:0031408: oxylipin biosynthetic process2.18E-02
137GO:0009735: response to cytokinin2.19E-02
138GO:0016226: iron-sulfur cluster assembly2.33E-02
139GO:0006730: one-carbon metabolic process2.33E-02
140GO:0007005: mitochondrion organization2.33E-02
141GO:0006396: RNA processing2.77E-02
142GO:0006508: proteolysis3.07E-02
143GO:0006814: sodium ion transport3.27E-02
144GO:0002229: defense response to oomycetes3.61E-02
145GO:0000302: response to reactive oxygen species3.61E-02
146GO:0032502: developmental process3.78E-02
147GO:0007264: small GTPase mediated signal transduction3.78E-02
148GO:0030163: protein catabolic process3.96E-02
149GO:0009409: response to cold4.17E-02
150GO:0040008: regulation of growth4.42E-02
151GO:0007623: circadian rhythm4.63E-02
RankGO TermAdjusted P value
1GO:0047513: 1,2-alpha-L-fucosidase 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:0045435: lycopene epsilon cyclase activity0.00E+00
5GO:0061711: N(6)-L-threonylcarbamoyladenine synthase0.00E+00
6GO:0004823: leucine-tRNA ligase activity0.00E+00
7GO:0008756: o-succinylbenzoate-CoA ligase activity0.00E+00
8GO:0005048: signal sequence binding0.00E+00
9GO:0009974: zeinoxanthin epsilon hydroxylase activity0.00E+00
10GO:0019843: rRNA binding2.68E-22
11GO:0003735: structural constituent of ribosome1.37E-13
12GO:0016851: magnesium chelatase activity2.35E-07
13GO:0016149: translation release factor activity, codon specific4.45E-05
14GO:0003755: peptidyl-prolyl cis-trans isomerase activity5.18E-05
15GO:0003723: RNA binding1.55E-04
16GO:0051920: peroxiredoxin activity2.41E-04
17GO:0050567: glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity3.57E-04
18GO:0001530: lipopolysaccharide binding3.57E-04
19GO:0004828: serine-tRNA ligase activity3.57E-04
20GO:0004853: uroporphyrinogen decarboxylase activity3.57E-04
21GO:0045485: omega-6 fatty acid desaturase activity3.57E-04
22GO:0004832: valine-tRNA ligase activity3.57E-04
23GO:0030785: [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity3.57E-04
24GO:0004820: glycine-tRNA ligase activity3.57E-04
25GO:0004328: formamidase activity3.57E-04
26GO:0004654: polyribonucleotide nucleotidyltransferase activity3.57E-04
27GO:0016209: antioxidant activity3.92E-04
28GO:0003747: translation release factor activity5.76E-04
29GO:0008839: 4-hydroxy-tetrahydrodipicolinate reductase7.77E-04
30GO:0004326: tetrahydrofolylpolyglutamate synthase activity7.77E-04
31GO:0009977: proton motive force dependent protein transmembrane transporter activity7.77E-04
32GO:0004617: phosphoglycerate dehydrogenase activity7.77E-04
33GO:0046509: 1,2-diacylglycerol 3-beta-galactosyltransferase activity7.77E-04
34GO:0008236: serine-type peptidase activity1.13E-03
35GO:0017150: tRNA dihydrouridine synthase activity1.26E-03
36GO:0003913: DNA photolyase activity1.26E-03
37GO:0002161: aminoacyl-tRNA editing activity1.26E-03
38GO:0004148: dihydrolipoyl dehydrogenase activity1.26E-03
39GO:0030267: glyoxylate reductase (NADP) activity1.26E-03
40GO:0008266: poly(U) RNA binding1.33E-03
41GO:0004222: metalloendopeptidase activity1.36E-03
42GO:0035250: UDP-galactosyltransferase activity1.81E-03
43GO:0016811: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides1.81E-03
44GO:0043023: ribosomal large subunit binding1.81E-03
45GO:0008097: 5S rRNA binding1.81E-03
46GO:0008508: bile acid:sodium symporter activity1.81E-03
47GO:0001872: (1->3)-beta-D-glucan binding1.81E-03
48GO:0004742: dihydrolipoyllysine-residue acetyltransferase activity1.81E-03
49GO:0016987: sigma factor activity2.44E-03
50GO:0043495: protein anchor2.44E-03
51GO:0003841: 1-acylglycerol-3-phosphate O-acyltransferase activity2.44E-03
52GO:0004659: prenyltransferase activity2.44E-03
53GO:0016279: protein-lysine N-methyltransferase activity2.44E-03
54GO:0001053: plastid sigma factor activity2.44E-03
55GO:0004345: glucose-6-phosphate dehydrogenase activity2.44E-03
56GO:0004045: aminoacyl-tRNA hydrolase activity2.44E-03
57GO:0004812: aminoacyl-tRNA ligase activity3.13E-03
58GO:0004519: endonuclease activity3.19E-03
59GO:0004130: cytochrome-c peroxidase activity3.85E-03
60GO:0004366: glycerol-3-phosphate O-acyltransferase activity3.85E-03
61GO:0016208: AMP binding3.85E-03
62GO:0005247: voltage-gated chloride channel activity3.85E-03
63GO:1990714: hydroxyproline O-galactosyltransferase activity3.85E-03
64GO:0045156: electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity4.64E-03
65GO:0015631: tubulin binding4.64E-03
66GO:0004616: phosphogluconate dehydrogenase (decarboxylating) activity4.64E-03
67GO:0009881: photoreceptor activity5.48E-03
68GO:0019899: enzyme binding5.48E-03
69GO:0004033: aldo-keto reductase (NADP) activity6.37E-03
70GO:0008312: 7S RNA binding6.37E-03
71GO:0003729: mRNA binding6.73E-03
72GO:0016705: oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen7.09E-03
73GO:0015450: P-P-bond-hydrolysis-driven protein transmembrane transporter activity8.51E-03
74GO:0003993: acid phosphatase activity1.13E-02
75GO:0044183: protein binding involved in protein folding1.15E-02
76GO:0004364: glutathione transferase activity1.34E-02
77GO:0000175: 3'-5'-exoribonuclease activity1.39E-02
78GO:0042973: glucan endo-1,3-beta-D-glucosidase activity1.51E-02
79GO:0004601: peroxidase activity1.80E-02
80GO:0016788: hydrolase activity, acting on ester bonds1.84E-02
81GO:0005528: FK506 binding1.90E-02
82GO:0051536: iron-sulfur cluster binding1.90E-02
83GO:0003690: double-stranded DNA binding1.95E-02
84GO:0043424: protein histidine kinase binding2.04E-02
85GO:0004176: ATP-dependent peptidase activity2.18E-02
86GO:0022891: substrate-specific transmembrane transporter activity2.48E-02
87GO:0003727: single-stranded RNA binding2.63E-02
88GO:0008080: N-acetyltransferase activity3.11E-02
89GO:0003713: transcription coactivator activity3.11E-02
90GO:0010181: FMN binding3.27E-02
91GO:0004252: serine-type endopeptidase activity3.73E-02
92GO:0003924: GTPase activity3.83E-02
93GO:0004675: transmembrane receptor protein serine/threonine kinase activity4.32E-02
94GO:0008237: metallopeptidase activity4.32E-02
95GO:0016597: amino acid binding4.50E-02
96GO:0016168: chlorophyll binding4.88E-02
RankGO TermAdjusted P value
1GO:0000408: EKC/KEOPS complex0.00E+00
2GO:0009507: chloroplast2.00E-72
3GO:0009570: chloroplast stroma1.39E-47
4GO:0009941: chloroplast envelope2.02E-32
5GO:0009535: chloroplast thylakoid membrane2.53E-19
6GO:0009579: thylakoid3.06E-15
7GO:0005840: ribosome4.78E-13
8GO:0009543: chloroplast thylakoid lumen6.06E-13
9GO:0009534: chloroplast thylakoid1.33E-09
10GO:0031977: thylakoid lumen2.96E-09
11GO:0010007: magnesium chelatase complex4.86E-08
12GO:0009533: chloroplast stromal thylakoid8.13E-06
13GO:0031969: chloroplast membrane5.31E-05
14GO:0000311: plastid large ribosomal subunit6.61E-05
15GO:0009536: plastid1.34E-04
16GO:0030956: glutamyl-tRNA(Gln) amidotransferase complex3.57E-04
17GO:0009344: nitrite reductase complex [NAD(P)H]3.57E-04
18GO:0009547: plastid ribosome3.57E-04
19GO:0010598: NAD(P)H dehydrogenase complex (plastoquinone)5.76E-04
20GO:0080085: signal recognition particle, chloroplast targeting7.77E-04
21GO:0030529: intracellular ribonucleoprotein complex8.65E-04
22GO:0009706: chloroplast inner membrane9.44E-04
23GO:0033281: TAT protein transport complex1.26E-03
24GO:0030095: chloroplast photosystem II1.33E-03
25GO:0000312: plastid small ribosomal subunit1.33E-03
26GO:0009654: photosystem II oxygen evolving complex2.03E-03
27GO:0042651: thylakoid membrane2.03E-03
28GO:0034707: chloride channel complex3.85E-03
29GO:0019898: extrinsic component of membrane4.20E-03
30GO:0022626: cytosolic ribosome6.96E-03
31GO:0005786: signal recognition particle, endoplasmic reticulum targeting7.30E-03
32GO:0005763: mitochondrial small ribosomal subunit8.29E-03
33GO:0009707: chloroplast outer membrane8.51E-03
34GO:0015934: large ribosomal subunit9.85E-03
35GO:0043231: intracellular membrane-bounded organelle1.23E-02
36GO:0032040: small-subunit processome1.27E-02
37GO:0046658: anchored component of plasma membrane1.48E-02
38GO:0043234: protein complex1.77E-02
39GO:0015935: small ribosomal subunit2.18E-02
40GO:0009532: plastid stroma2.18E-02
41GO:0022625: cytosolic large ribosomal subunit2.52E-02
42GO:0010287: plastoglobule3.19E-02
43GO:0009523: photosystem II3.44E-02
44GO:0005759: mitochondrial matrix4.22E-02
45GO:0009295: nucleoid4.32E-02
46GO:0005778: peroxisomal membrane4.32E-02
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Gene type



Gene DE type