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

AT3G54660

GO-BP
GO-MF
GO-CC
RankGO TermAdjusted P value
1GO:2000469: negative regulation of peroxidase activity0.00E+00
2GO:0010059: positive regulation of atrichoblast fate specification0.00E+00
3GO:0017038: protein import0.00E+00
4GO:0090697: post-embryonic plant organ morphogenesis0.00E+00
5GO:0042821: pyridoxal biosynthetic process0.00E+00
6GO:0042820: vitamin B6 catabolic process0.00E+00
7GO:0015882: L-ascorbic acid transport0.00E+00
8GO:1905177: tracheary element differentiation0.00E+00
9GO:0018023: peptidyl-lysine trimethylation0.00E+00
10GO:0009658: chloroplast organization1.52E-06
11GO:1900871: chloroplast mRNA modification1.01E-05
12GO:1902326: positive regulation of chlorophyll biosynthetic process1.01E-05
13GO:0010583: response to cyclopentenone1.17E-04
14GO:0045038: protein import into chloroplast thylakoid membrane1.98E-04
15GO:0009416: response to light stimulus4.76E-04
16GO:0015904: tetracycline transport4.78E-04
17GO:2000905: negative regulation of starch metabolic process4.78E-04
18GO:0005991: trehalose metabolic process4.78E-04
19GO:0006419: alanyl-tRNA aminoacylation4.78E-04
20GO:0009443: pyridoxal 5'-phosphate salvage4.78E-04
21GO:0080173: male-female gamete recognition during double fertilization4.78E-04
22GO:1905039: carboxylic acid transmembrane transport4.78E-04
23GO:1905200: gibberellic acid transmembrane transport4.78E-04
24GO:0080112: seed growth4.78E-04
25GO:0030198: extracellular matrix organization4.78E-04
26GO:1904966: positive regulation of vitamin E biosynthetic process4.78E-04
27GO:0046520: sphingoid biosynthetic process4.78E-04
28GO:0043266: regulation of potassium ion transport4.78E-04
29GO:0010063: positive regulation of trichoblast fate specification4.78E-04
30GO:0010480: microsporocyte differentiation4.78E-04
31GO:0051775: response to redox state4.78E-04
32GO:0006659: phosphatidylserine biosynthetic process4.78E-04
33GO:1904964: positive regulation of phytol biosynthetic process4.78E-04
34GO:2000021: regulation of ion homeostasis4.78E-04
35GO:0070574: cadmium ion transmembrane transport4.78E-04
36GO:0051247: positive regulation of protein metabolic process4.78E-04
37GO:1902458: positive regulation of stomatal opening4.78E-04
38GO:0010028: xanthophyll cycle4.78E-04
39GO:0048437: floral organ development4.82E-04
40GO:0030307: positive regulation of cell growth4.82E-04
41GO:0046620: regulation of organ growth6.01E-04
42GO:0010182: sugar mediated signaling pathway7.16E-04
43GO:0009646: response to absence of light7.86E-04
44GO:1903426: regulation of reactive oxygen species biosynthetic process1.03E-03
45GO:0006568: tryptophan metabolic process1.03E-03
46GO:0010024: phytochromobilin biosynthetic process1.03E-03
47GO:0051645: Golgi localization1.03E-03
48GO:0060359: response to ammonium ion1.03E-03
49GO:0048255: mRNA stabilization1.03E-03
50GO:1900865: chloroplast RNA modification1.03E-03
51GO:1901959: positive regulation of cutin biosynthetic process1.03E-03
52GO:0018026: peptidyl-lysine monomethylation1.03E-03
53GO:0060151: peroxisome localization1.03E-03
54GO:0071497: cellular response to freezing1.03E-03
55GO:1904143: positive regulation of carotenoid biosynthetic process1.03E-03
56GO:0009773: photosynthetic electron transport in photosystem I1.39E-03
57GO:0010027: thylakoid membrane organization1.49E-03
58GO:0033591: response to L-ascorbic acid1.68E-03
59GO:0048586: regulation of long-day photoperiodism, flowering1.68E-03
60GO:0006954: inflammatory response1.68E-03
61GO:0006788: heme oxidation1.68E-03
62GO:0051646: mitochondrion localization1.68E-03
63GO:0090436: leaf pavement cell development1.68E-03
64GO:0010623: programmed cell death involved in cell development1.68E-03
65GO:1904278: positive regulation of wax biosynthetic process1.68E-03
66GO:0090153: regulation of sphingolipid biosynthetic process1.68E-03
67GO:0043157: response to cation stress1.68E-03
68GO:0072661: protein targeting to plasma membrane1.68E-03
69GO:0005977: glycogen metabolic process1.68E-03
70GO:0030048: actin filament-based movement1.80E-03
71GO:0010588: cotyledon vascular tissue pattern formation1.80E-03
72GO:0010207: photosystem II assembly2.04E-03
73GO:0010371: regulation of gibberellin biosynthetic process2.44E-03
74GO:0010071: root meristem specification2.44E-03
75GO:0009102: biotin biosynthetic process2.44E-03
76GO:0006107: oxaloacetate metabolic process2.44E-03
77GO:0010239: chloroplast mRNA processing2.44E-03
78GO:0019048: modulation by virus of host morphology or physiology2.44E-03
79GO:0031048: chromatin silencing by small RNA2.44E-03
80GO:0016556: mRNA modification2.44E-03
81GO:0043572: plastid fission2.44E-03
82GO:0090308: regulation of methylation-dependent chromatin silencing2.44E-03
83GO:0010258: NADH dehydrogenase complex (plastoquinone) assembly2.44E-03
84GO:0005975: carbohydrate metabolic process2.62E-03
85GO:0009734: auxin-activated signaling pathway3.27E-03
86GO:0010109: regulation of photosynthesis3.28E-03
87GO:0009765: photosynthesis, light harvesting3.28E-03
88GO:2000306: positive regulation of photomorphogenesis3.28E-03
89GO:0006109: regulation of carbohydrate metabolic process3.28E-03
90GO:0045723: positive regulation of fatty acid biosynthetic process3.28E-03
91GO:0006021: inositol biosynthetic process3.28E-03
92GO:0051567: histone H3-K9 methylation3.28E-03
93GO:0010508: positive regulation of autophagy3.28E-03
94GO:0008295: spermidine biosynthetic process3.28E-03
95GO:0006734: NADH metabolic process3.28E-03
96GO:0010021: amylopectin biosynthetic process3.28E-03
97GO:1901141: regulation of lignin biosynthetic process3.28E-03
98GO:0030245: cellulose catabolic process3.76E-03
99GO:0016123: xanthophyll biosynthetic process4.21E-03
100GO:0080110: sporopollenin biosynthetic process4.21E-03
101GO:0009451: RNA modification4.38E-03
102GO:0006855: drug transmembrane transport4.76E-03
103GO:0010264: myo-inositol hexakisphosphate biosynthetic process5.21E-03
104GO:0009959: negative gravitropism5.21E-03
105GO:0016554: cytidine to uridine editing5.21E-03
106GO:0000741: karyogamy5.21E-03
107GO:0016458: gene silencing5.21E-03
108GO:0019243: methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione5.21E-03
109GO:0010305: leaf vascular tissue pattern formation5.64E-03
110GO:0080086: stamen filament development6.28E-03
111GO:0048280: vesicle fusion with Golgi apparatus6.28E-03
112GO:2000033: regulation of seed dormancy process6.28E-03
113GO:1901259: chloroplast rRNA processing6.28E-03
114GO:0030488: tRNA methylation6.28E-03
115GO:0010189: vitamin E biosynthetic process6.28E-03
116GO:0009791: post-embryonic development6.51E-03
117GO:0008654: phospholipid biosynthetic process6.51E-03
118GO:0048367: shoot system development7.39E-03
119GO:0000122: negative regulation of transcription from RNA polymerase II promoter7.43E-03
120GO:0006400: tRNA modification7.43E-03
121GO:0032502: developmental process7.45E-03
122GO:0010090: trichome morphogenesis7.95E-03
123GO:0010252: auxin homeostasis8.47E-03
124GO:0052543: callose deposition in cell wall8.65E-03
125GO:0048564: photosystem I assembly8.65E-03
126GO:0009690: cytokinin metabolic process8.65E-03
127GO:0006605: protein targeting8.65E-03
128GO:0070413: trehalose metabolism in response to stress8.65E-03
129GO:0006875: cellular metal ion homeostasis8.65E-03
130GO:2000070: regulation of response to water deprivation8.65E-03
131GO:0009733: response to auxin9.48E-03
132GO:0015996: chlorophyll catabolic process9.94E-03
133GO:0007186: G-protein coupled receptor signaling pathway9.94E-03
134GO:0009657: plastid organization9.94E-03
135GO:0048366: leaf development1.05E-02
136GO:0098656: anion transmembrane transport1.13E-02
137GO:0000373: Group II intron splicing1.13E-02
138GO:0000902: cell morphogenesis1.13E-02
139GO:0007169: transmembrane receptor protein tyrosine kinase signaling pathway1.20E-02
140GO:0009638: phototropism1.27E-02
141GO:0031425: chloroplast RNA processing1.27E-02
142GO:0031627: telomeric loop formation1.42E-02
143GO:0010162: seed dormancy process1.42E-02
144GO:0009299: mRNA transcription1.42E-02
145GO:0006896: Golgi to vacuole transport1.42E-02
146GO:0030422: production of siRNA involved in RNA interference1.42E-02
147GO:0048829: root cap development1.42E-02
148GO:0010015: root morphogenesis1.57E-02
149GO:0019684: photosynthesis, light reaction1.57E-02
150GO:0009089: lysine biosynthetic process via diaminopimelate1.57E-02
151GO:0009073: aromatic amino acid family biosynthetic process1.57E-02
152GO:0043085: positive regulation of catalytic activity1.57E-02
153GO:0015770: sucrose transport1.57E-02
154GO:0006415: translational termination1.57E-02
155GO:0048229: gametophyte development1.57E-02
156GO:0010216: maintenance of DNA methylation1.57E-02
157GO:0006865: amino acid transport1.61E-02
158GO:0040008: regulation of growth1.70E-02
159GO:0045037: protein import into chloroplast stroma1.73E-02
160GO:0009725: response to hormone1.90E-02
161GO:2000012: regulation of auxin polar transport1.90E-02
162GO:0010628: positive regulation of gene expression1.90E-02
163GO:0010102: lateral root morphogenesis1.90E-02
164GO:0006108: malate metabolic process1.90E-02
165GO:0009718: anthocyanin-containing compound biosynthetic process1.90E-02
166GO:0010075: regulation of meristem growth1.90E-02
167GO:0016042: lipid catabolic process1.96E-02
168GO:0009934: regulation of meristem structural organization2.07E-02
169GO:0048467: gynoecium development2.07E-02
170GO:0010020: chloroplast fission2.07E-02
171GO:0009887: animal organ morphogenesis2.07E-02
172GO:0051707: response to other organism2.17E-02
173GO:0019853: L-ascorbic acid biosynthetic process2.24E-02
174GO:0009901: anther dehiscence2.24E-02
175GO:0010030: positive regulation of seed germination2.24E-02
176GO:0006071: glycerol metabolic process2.42E-02
177GO:0019762: glucosinolate catabolic process2.42E-02
178GO:0005992: trehalose biosynthetic process2.61E-02
179GO:0019953: sexual reproduction2.80E-02
180GO:0007017: microtubule-based process2.80E-02
181GO:0010431: seed maturation2.99E-02
182GO:0031408: oxylipin biosynthetic process2.99E-02
183GO:0006306: DNA methylation2.99E-02
184GO:0003333: amino acid transmembrane transport2.99E-02
185GO:0007275: multicellular organism development3.05E-02
186GO:0031348: negative regulation of defense response3.19E-02
187GO:0006012: galactose metabolic process3.40E-02
188GO:0009686: gibberellin biosynthetic process3.40E-02
189GO:0010089: xylem development3.60E-02
190GO:0010584: pollen exine formation3.60E-02
191GO:0042127: regulation of cell proliferation3.60E-02
192GO:0009789: positive regulation of abscisic acid-activated signaling pathway3.82E-02
193GO:0042147: retrograde transport, endosome to Golgi3.82E-02
194GO:0009740: gibberellic acid mediated signaling pathway3.92E-02
195GO:0010118: stomatal movement4.03E-02
196GO:0048653: anther development4.03E-02
197GO:0042631: cellular response to water deprivation4.03E-02
198GO:0080022: primary root development4.03E-02
199GO:0010087: phloem or xylem histogenesis4.03E-02
200GO:0006810: transport4.12E-02
201GO:0006342: chromatin silencing4.25E-02
202GO:0009741: response to brassinosteroid4.25E-02
203GO:0010268: brassinosteroid homeostasis4.25E-02
204GO:0010154: fruit development4.25E-02
205GO:0006662: glycerol ether metabolic process4.25E-02
206GO:0010197: polar nucleus fusion4.25E-02
207GO:0048868: pollen tube development4.25E-02
208GO:0006396: RNA processing4.29E-02
209GO:0009742: brassinosteroid mediated signaling pathway4.41E-02
210GO:0048544: recognition of pollen4.48E-02
211GO:0006623: protein targeting to vacuole4.71E-02
212GO:0019252: starch biosynthetic process4.71E-02
213GO:0055072: iron ion homeostasis4.71E-02
214GO:0015979: photosynthesis4.79E-02
215GO:0006891: intra-Golgi vesicle-mediated transport4.94E-02
216GO:0016132: brassinosteroid biosynthetic process4.94E-02
RankGO TermAdjusted P value
1GO:0005201: extracellular matrix structural constituent0.00E+00
2GO:0004076: biotin synthase activity0.00E+00
3GO:0010349: L-galactose dehydrogenase activity0.00E+00
4GO:0047513: 1,2-alpha-L-fucosidase activity0.00E+00
5GO:0046554: malate dehydrogenase (NADP+) activity0.00E+00
6GO:0050236: pyridoxine:NADP 4-dehydrogenase activity0.00E+00
7GO:0010276: phytol kinase activity0.00E+00
8GO:0015229: L-ascorbic acid transporter activity0.00E+00
9GO:0000170: sphingosine hydroxylase activity4.78E-04
10GO:0050139: nicotinate-N-glucosyltransferase activity4.78E-04
11GO:0004425: indole-3-glycerol-phosphate synthase activity4.78E-04
12GO:1905201: gibberellin transmembrane transporter activity4.78E-04
13GO:0051777: ent-kaurenoate oxidase activity4.78E-04
14GO:0004813: alanine-tRNA ligase activity4.78E-04
15GO:0008158: hedgehog receptor activity4.78E-04
16GO:0005080: protein kinase C binding4.78E-04
17GO:0030785: [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity4.78E-04
18GO:0008746: NAD(P)+ transhydrogenase activity4.78E-04
19GO:0004033: aldo-keto reductase (NADP) activity6.01E-04
20GO:0043425: bHLH transcription factor binding1.03E-03
21GO:0004766: spermidine synthase activity1.03E-03
22GO:0019156: isoamylase activity1.03E-03
23GO:0042284: sphingolipid delta-4 desaturase activity1.03E-03
24GO:0008839: 4-hydroxy-tetrahydrodipicolinate reductase1.03E-03
25GO:0008493: tetracycline transporter activity1.03E-03
26GO:0003988: acetyl-CoA C-acyltransferase activity1.03E-03
27GO:0004512: inositol-3-phosphate synthase activity1.03E-03
28GO:0017118: lipoyltransferase activity1.03E-03
29GO:0005215: transporter activity1.16E-03
30GO:0000976: transcription regulatory region sequence-specific DNA binding1.59E-03
31GO:0015462: ATPase-coupled protein transmembrane transporter activity1.68E-03
32GO:0003913: DNA photolyase activity1.68E-03
33GO:0070402: NADPH binding1.68E-03
34GO:0004519: endonuclease activity1.96E-03
35GO:0003774: motor activity2.04E-03
36GO:0042973: glucan endo-1,3-beta-D-glucosidase activity2.04E-03
37GO:0015238: drug transmembrane transporter activity2.22E-03
38GO:0004222: metalloendopeptidase activity2.37E-03
39GO:0003825: alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity2.44E-03
40GO:0015086: cadmium ion transmembrane transporter activity2.44E-03
41GO:0016149: translation release factor activity, codon specific2.44E-03
42GO:0035197: siRNA binding2.44E-03
43GO:0005345: purine nucleobase transmembrane transporter activity3.12E-03
44GO:0016655: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor3.28E-03
45GO:0043495: protein anchor3.28E-03
46GO:0004392: heme oxygenase (decyclizing) activity3.28E-03
47GO:0016279: protein-lysine N-methyltransferase activity3.28E-03
48GO:0008810: cellulase activity4.10E-03
49GO:0005275: amine transmembrane transporter activity4.21E-03
50GO:0016773: phosphotransferase activity, alcohol group as acceptor4.21E-03
51GO:0008514: organic anion transmembrane transporter activity4.46E-03
52GO:0004605: phosphatidate cytidylyltransferase activity5.21E-03
53GO:0004556: alpha-amylase activity5.21E-03
54GO:0004462: lactoylglutathione lyase activity5.21E-03
55GO:0016615: malate dehydrogenase activity5.21E-03
56GO:0008200: ion channel inhibitor activity5.21E-03
57GO:0008195: phosphatidate phosphatase activity6.28E-03
58GO:0030060: L-malate dehydrogenase activity6.28E-03
59GO:0004723: calcium-dependent protein serine/threonine phosphatase activity6.28E-03
60GO:0019899: enzyme binding7.43E-03
61GO:0015103: inorganic anion transmembrane transporter activity7.43E-03
62GO:0016788: hydrolase activity, acting on ester bonds8.46E-03
63GO:0008173: RNA methyltransferase activity9.94E-03
64GO:0008889: glycerophosphodiester phosphodiesterase activity1.13E-02
65GO:0003747: translation release factor activity1.13E-02
66GO:0052689: carboxylic ester hydrolase activity1.33E-02
67GO:0008047: enzyme activator activity1.42E-02
68GO:0015020: glucuronosyltransferase activity1.42E-02
69GO:0030234: enzyme regulator activity1.42E-02
70GO:0003691: double-stranded telomeric DNA binding1.57E-02
71GO:0008515: sucrose transmembrane transporter activity1.57E-02
72GO:0008559: xenobiotic-transporting ATPase activity1.57E-02
73GO:0004871: signal transducer activity1.61E-02
74GO:0015297: antiporter activity1.70E-02
75GO:0004521: endoribonuclease activity1.73E-02
76GO:0000049: tRNA binding1.73E-02
77GO:0003993: acid phosphatase activity1.76E-02
78GO:0004712: protein serine/threonine/tyrosine kinase activity1.84E-02
79GO:0003725: double-stranded RNA binding1.90E-02
80GO:0005315: inorganic phosphate transmembrane transporter activity1.90E-02
81GO:0031072: heat shock protein binding1.90E-02
82GO:0008146: sulfotransferase activity2.24E-02
83GO:0051119: sugar transmembrane transporter activity2.24E-02
84GO:0042802: identical protein binding2.45E-02
85GO:0004857: enzyme inhibitor activity2.61E-02
86GO:0005528: FK506 binding2.61E-02
87GO:0004176: ATP-dependent peptidase activity2.99E-02
88GO:0033612: receptor serine/threonine kinase binding2.99E-02
89GO:0015171: amino acid transmembrane transporter activity3.25E-02
90GO:0022891: substrate-specific transmembrane transporter activity3.40E-02
91GO:0003727: single-stranded RNA binding3.60E-02
92GO:0003723: RNA binding3.70E-02
93GO:0004650: polygalacturonase activity3.81E-02
94GO:0047134: protein-disulfide reductase activity3.82E-02
95GO:0008080: N-acetyltransferase activity4.25E-02
96GO:0046873: metal ion transmembrane transporter activity4.25E-02
97GO:0004791: thioredoxin-disulfide reductase activity4.48E-02
98GO:0050662: coenzyme binding4.48E-02
99GO:0048038: quinone binding4.94E-02
RankGO TermAdjusted P value
1GO:0010368: chloroplast isoamylase complex0.00E+00
2GO:0009507: chloroplast4.76E-08
3GO:0009570: chloroplast stroma2.01E-04
4GO:0010598: NAD(P)H dehydrogenase complex (plastoquinone)8.76E-04
5GO:0080085: signal recognition particle, chloroplast targeting1.03E-03
6GO:0016459: myosin complex1.20E-03
7GO:0005886: plasma membrane1.33E-03
8GO:0046658: anchored component of plasma membrane1.55E-03
9GO:0009528: plastid inner membrane1.68E-03
10GO:0019897: extrinsic component of plasma membrane1.68E-03
11GO:0009706: chloroplast inner membrane1.83E-03
12GO:0005719: nuclear euchromatin2.44E-03
13GO:0030658: transport vesicle membrane2.44E-03
14GO:0009527: plastid outer membrane3.28E-03
15GO:0009535: chloroplast thylakoid membrane7.05E-03
16GO:0012507: ER to Golgi transport vesicle membrane8.65E-03
17GO:0010319: stromule9.00E-03
18GO:0000783: nuclear telomere cap complex9.94E-03
19GO:0005786: signal recognition particle, endoplasmic reticulum targeting9.94E-03
20GO:0045298: tubulin complex1.13E-02
21GO:0005720: nuclear heterochromatin1.13E-02
22GO:0031225: anchored component of membrane1.23E-02
23GO:0015030: Cajal body1.27E-02
24GO:0000418: DNA-directed RNA polymerase IV complex1.42E-02
25GO:0016021: integral component of membrane1.57E-02
26GO:0009508: plastid chromosome1.90E-02
27GO:0031902: late endosome membrane2.00E-02
28GO:0009941: chloroplast envelope2.03E-02
29GO:0043231: intracellular membrane-bounded organelle2.37E-02
30GO:0042651: thylakoid membrane2.80E-02
31GO:0009532: plastid stroma2.99E-02
32GO:0009505: plant-type cell wall3.09E-02
33GO:0031969: chloroplast membrane4.08E-02
34GO:0016020: membrane4.15E-02
35GO:0005770: late endosome4.25E-02
36GO:0009523: photosystem II4.71E-02
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Gene type



Gene DE type