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

AT3G04960

GO-BP
GO-MF
GO-CC
RankGO TermAdjusted P value
1GO:0017038: protein import0.00E+00
2GO:0046838: phosphorylated carbohydrate dephosphorylation0.00E+00
3GO:1903224: regulation of endodermal cell differentiation0.00E+00
4GO:2000042: negative regulation of double-strand break repair via homologous recombination0.00E+00
5GO:0042407: cristae formation0.00E+00
6GO:1905255: regulation of RNA binding transcription factor activity0.00E+00
7GO:0045184: establishment of protein localization0.00E+00
8GO:0018023: peptidyl-lysine trimethylation0.00E+00
9GO:0031222: arabinan catabolic process0.00E+00
10GO:0006429: leucyl-tRNA aminoacylation0.00E+00
11GO:0042352: GDP-L-fucose salvage0.00E+00
12GO:0061157: mRNA destabilization0.00E+00
13GO:0043392: negative regulation of DNA binding0.00E+00
14GO:0010059: positive regulation of atrichoblast fate specification0.00E+00
15GO:0032194: ubiquinone biosynthetic process via 3,4-dihydroxy-5-polyprenylbenzoate0.00E+00
16GO:0018026: peptidyl-lysine monomethylation9.75E-06
17GO:0009416: response to light stimulus2.20E-05
18GO:0005983: starch catabolic process1.21E-04
19GO:0042793: transcription from plastid promoter2.73E-04
20GO:0042372: phylloquinone biosynthetic process3.65E-04
21GO:0009658: chloroplast organization4.69E-04
22GO:0019294: keto-3-deoxy-D-manno-octulosonic acid biosynthetic process4.70E-04
23GO:1905039: carboxylic acid transmembrane transport4.70E-04
24GO:1905200: gibberellic acid transmembrane transport4.70E-04
25GO:0048437: floral organ development4.70E-04
26GO:0046900: tetrahydrofolylpolyglutamate metabolic process4.70E-04
27GO:0080112: seed growth4.70E-04
28GO:0005980: glycogen catabolic process4.70E-04
29GO:0030198: extracellular matrix organization4.70E-04
30GO:0010063: positive regulation of trichoblast fate specification4.70E-04
31GO:0090558: plant epidermis development4.70E-04
32GO:0046520: sphingoid biosynthetic process4.70E-04
33GO:0010480: microsporocyte differentiation4.70E-04
34GO:0042371: vitamin K biosynthetic process4.70E-04
35GO:0043686: co-translational protein modification4.70E-04
36GO:0035987: endodermal cell differentiation4.70E-04
37GO:0043007: maintenance of rDNA4.70E-04
38GO:0015904: tetracycline transport4.70E-04
39GO:0000023: maltose metabolic process4.70E-04
40GO:0042659: regulation of cell fate specification4.70E-04
41GO:0000025: maltose catabolic process4.70E-04
42GO:0046620: regulation of organ growth5.86E-04
43GO:0006662: glycerol ether metabolic process6.93E-04
44GO:0010305: leaf vascular tissue pattern formation6.93E-04
45GO:0009741: response to brassinosteroid6.93E-04
46GO:0009098: leucine biosynthetic process1.01E-03
47GO:1900871: chloroplast mRNA modification1.01E-03
48GO:1900865: chloroplast RNA modification1.01E-03
49GO:1902326: positive regulation of chlorophyll biosynthetic process1.01E-03
50GO:0030187: melatonin biosynthetic process1.01E-03
51GO:0006432: phenylalanyl-tRNA aminoacylation1.01E-03
52GO:0007154: cell communication1.01E-03
53GO:0071497: cellular response to freezing1.01E-03
54GO:1900033: negative regulation of trichome patterning1.01E-03
55GO:0042325: regulation of phosphorylation1.01E-03
56GO:0006423: cysteinyl-tRNA aminoacylation1.01E-03
57GO:1904143: positive regulation of carotenoid biosynthetic process1.01E-03
58GO:0031648: protein destabilization1.01E-03
59GO:0001682: tRNA 5'-leader removal1.01E-03
60GO:0006568: tryptophan metabolic process1.01E-03
61GO:0009629: response to gravity1.01E-03
62GO:0009773: photosynthetic electron transport in photosystem I1.35E-03
63GO:0010027: thylakoid membrane organization1.44E-03
64GO:0009405: pathogenesis1.65E-03
65GO:0071398: cellular response to fatty acid1.65E-03
66GO:0033591: response to L-ascorbic acid1.65E-03
67GO:0090708: specification of plant organ axis polarity1.65E-03
68GO:0046739: transport of virus in multicellular host2.39E-03
69GO:0043433: negative regulation of sequence-specific DNA binding transcription factor activity2.39E-03
70GO:0043572: plastid fission2.39E-03
71GO:0016556: mRNA modification2.39E-03
72GO:0010321: regulation of vegetative phase change2.39E-03
73GO:0010371: regulation of gibberellin biosynthetic process2.39E-03
74GO:0010071: root meristem specification2.39E-03
75GO:0009102: biotin biosynthetic process2.39E-03
76GO:0010306: rhamnogalacturonan II biosynthetic process2.39E-03
77GO:0034599: cellular response to oxidative stress2.89E-03
78GO:0006221: pyrimidine nucleotide biosynthetic process3.22E-03
79GO:0009733: response to auxin3.22E-03
80GO:0009755: hormone-mediated signaling pathway3.22E-03
81GO:1901141: regulation of lignin biosynthetic process3.22E-03
82GO:0048629: trichome patterning3.22E-03
83GO:0010109: regulation of photosynthesis3.22E-03
84GO:0042274: ribosomal small subunit biogenesis3.22E-03
85GO:0030104: water homeostasis3.22E-03
86GO:0009640: photomorphogenesis3.78E-03
87GO:0016131: brassinosteroid metabolic process4.13E-03
88GO:0032543: mitochondrial translation4.13E-03
89GO:0010236: plastoquinone biosynthetic process4.13E-03
90GO:0031365: N-terminal protein amino acid modification4.13E-03
91GO:0010438: cellular response to sulfur starvation4.13E-03
92GO:0006855: drug transmembrane transport4.60E-03
93GO:0008033: tRNA processing5.09E-03
94GO:1902456: regulation of stomatal opening5.11E-03
95GO:0048831: regulation of shoot system development5.11E-03
96GO:0016554: cytidine to uridine editing5.11E-03
97GO:0006086: acetyl-CoA biosynthetic process from pyruvate5.11E-03
98GO:0018258: protein O-linked glycosylation via hydroxyproline5.11E-03
99GO:0000741: karyogamy5.11E-03
100GO:0010405: arabinogalactan protein metabolic process5.11E-03
101GO:0009959: negative gravitropism5.11E-03
102GO:0010197: polar nucleus fusion5.49E-03
103GO:0009646: response to absence of light5.91E-03
104GO:0006857: oligopeptide transport6.04E-03
105GO:0009082: branched-chain amino acid biosynthetic process6.17E-03
106GO:0006458: 'de novo' protein folding6.17E-03
107GO:0048280: vesicle fusion with Golgi apparatus6.17E-03
108GO:0042026: protein refolding6.17E-03
109GO:0048509: regulation of meristem development6.17E-03
110GO:0009099: valine biosynthetic process6.17E-03
111GO:0030488: tRNA methylation6.17E-03
112GO:2000033: regulation of seed dormancy process6.17E-03
113GO:1901259: chloroplast rRNA processing6.17E-03
114GO:0031930: mitochondria-nucleus signaling pathway6.17E-03
115GO:0080086: stamen filament development6.17E-03
116GO:2000067: regulation of root morphogenesis6.17E-03
117GO:0016032: viral process7.26E-03
118GO:0010583: response to cyclopentenone7.26E-03
119GO:0010161: red light signaling pathway7.30E-03
120GO:0006955: immune response7.30E-03
121GO:0009772: photosynthetic electron transport in photosystem II7.30E-03
122GO:1901657: glycosyl compound metabolic process7.74E-03
123GO:0010439: regulation of glucosinolate biosynthetic process8.49E-03
124GO:0009819: drought recovery8.49E-03
125GO:0006605: protein targeting8.49E-03
126GO:0009704: de-etiolation8.49E-03
127GO:2000070: regulation of response to water deprivation8.49E-03
128GO:0055075: potassium ion homeostasis8.49E-03
129GO:0000105: histidine biosynthetic process8.49E-03
130GO:0052543: callose deposition in cell wall8.49E-03
131GO:0009742: brassinosteroid mediated signaling pathway9.37E-03
132GO:0009097: isoleucine biosynthetic process9.75E-03
133GO:0010100: negative regulation of photomorphogenesis9.75E-03
134GO:0009657: plastid organization9.75E-03
135GO:0010099: regulation of photomorphogenesis9.75E-03
136GO:0006783: heme biosynthetic process1.11E-02
137GO:0048507: meristem development1.11E-02
138GO:0000902: cell morphogenesis1.11E-02
139GO:0046685: response to arsenic-containing substance1.11E-02
140GO:0051865: protein autoubiquitination1.11E-02
141GO:0007169: transmembrane receptor protein tyrosine kinase signaling pathway1.15E-02
142GO:0015995: chlorophyll biosynthetic process1.16E-02
143GO:0031425: chloroplast RNA processing1.25E-02
144GO:0009638: phototropism1.25E-02
145GO:0043067: regulation of programmed cell death1.25E-02
146GO:2000280: regulation of root development1.25E-02
147GO:0006896: Golgi to vacuole transport1.39E-02
148GO:0016441: posttranscriptional gene silencing1.39E-02
149GO:0010162: seed dormancy process1.39E-02
150GO:0009790: embryo development1.41E-02
151GO:0045454: cell redox homeostasis1.44E-02
152GO:0009073: aromatic amino acid family biosynthetic process1.54E-02
153GO:0043085: positive regulation of catalytic activity1.54E-02
154GO:0009682: induced systemic resistance1.54E-02
155GO:0000272: polysaccharide catabolic process1.54E-02
156GO:0015770: sucrose transport1.54E-02
157GO:0048229: gametophyte development1.54E-02
158GO:0010015: root morphogenesis1.54E-02
159GO:0000038: very long-chain fatty acid metabolic process1.54E-02
160GO:0010105: negative regulation of ethylene-activated signaling pathway1.70E-02
161GO:0009793: embryo development ending in seed dormancy1.73E-02
162GO:0009451: RNA modification1.80E-02
163GO:0010588: cotyledon vascular tissue pattern formation1.86E-02
164GO:0010628: positive regulation of gene expression1.86E-02
165GO:0010102: lateral root morphogenesis1.86E-02
166GO:0006006: glucose metabolic process1.86E-02
167GO:0009691: cytokinin biosynthetic process1.86E-02
168GO:0009718: anthocyanin-containing compound biosynthetic process1.86E-02
169GO:0010075: regulation of meristem growth1.86E-02
170GO:0009767: photosynthetic electron transport chain1.86E-02
171GO:0006631: fatty acid metabolic process1.95E-02
172GO:0006541: glutamine metabolic process2.03E-02
173GO:0010020: chloroplast fission2.03E-02
174GO:0009266: response to temperature stimulus2.03E-02
175GO:0009934: regulation of meristem structural organization2.03E-02
176GO:0007166: cell surface receptor signaling pathway2.07E-02
177GO:0019853: L-ascorbic acid biosynthetic process2.20E-02
178GO:0009901: anther dehiscence2.20E-02
179GO:0090351: seedling development2.20E-02
180GO:0010030: positive regulation of seed germination2.20E-02
181GO:0006071: glycerol metabolic process2.38E-02
182GO:0006833: water transport2.38E-02
183GO:0019762: glucosinolate catabolic process2.38E-02
184GO:0000162: tryptophan biosynthetic process2.38E-02
185GO:0080147: root hair cell development2.56E-02
186GO:0010187: negative regulation of seed germination2.56E-02
187GO:0005992: trehalose biosynthetic process2.56E-02
188GO:0006418: tRNA aminoacylation for protein translation2.74E-02
189GO:0051302: regulation of cell division2.74E-02
190GO:0048278: vesicle docking2.94E-02
191GO:0016998: cell wall macromolecule catabolic process2.94E-02
192GO:0048511: rhythmic process2.94E-02
193GO:0010431: seed maturation2.94E-02
194GO:0061077: chaperone-mediated protein folding2.94E-02
195GO:2000022: regulation of jasmonic acid mediated signaling pathway3.13E-02
196GO:0006730: one-carbon metabolic process3.13E-02
197GO:0031348: negative regulation of defense response3.13E-02
198GO:0009734: auxin-activated signaling pathway3.27E-02
199GO:0009693: ethylene biosynthetic process3.33E-02
200GO:0009686: gibberellin biosynthetic process3.33E-02
201GO:0009625: response to insect3.33E-02
202GO:0006012: galactose metabolic process3.33E-02
203GO:0048367: shoot system development3.49E-02
204GO:0042127: regulation of cell proliferation3.54E-02
205GO:0042147: retrograde transport, endosome to Golgi3.74E-02
206GO:0009789: positive regulation of abscisic acid-activated signaling pathway3.74E-02
207GO:0080022: primary root development3.96E-02
208GO:0042335: cuticle development3.96E-02
209GO:0010087: phloem or xylem histogenesis3.96E-02
210GO:0010118: stomatal movement3.96E-02
211GO:0048653: anther development3.96E-02
212GO:0042631: cellular response to water deprivation3.96E-02
213GO:0009960: endosperm development4.17E-02
214GO:0010182: sugar mediated signaling pathway4.17E-02
215GO:0048868: pollen tube development4.17E-02
216GO:0005975: carbohydrate metabolic process4.17E-02
217GO:0010268: brassinosteroid homeostasis4.17E-02
218GO:0061025: membrane fusion4.39E-02
219GO:0042752: regulation of circadian rhythm4.39E-02
220GO:0006623: protein targeting to vacuole4.62E-02
221GO:0006891: intra-Golgi vesicle-mediated transport4.85E-02
RankGO TermAdjusted P value
1GO:0050201: fucokinase activity0.00E+00
2GO:0046428: 1,4-dihydroxy-2-naphthoate octaprenyltransferase activity0.00E+00
3GO:0004823: leucine-tRNA ligase activity0.00E+00
4GO:0008756: o-succinylbenzoate-CoA ligase activity0.00E+00
5GO:0003949: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity0.00E+00
6GO:0005201: extracellular matrix structural constituent0.00E+00
7GO:0047341: fucose-1-phosphate guanylyltransferase activity0.00E+00
8GO:0004076: biotin synthase activity0.00E+00
9GO:0004059: aralkylamine N-acetyltransferase activity0.00E+00
10GO:0010349: L-galactose dehydrogenase activity0.00E+00
11GO:0071633: dihydroceramidase activity0.00E+00
12GO:0005363: maltose transmembrane transporter activity0.00E+00
13GO:0016279: protein-lysine N-methyltransferase activity1.25E-04
14GO:0004134: 4-alpha-glucanotransferase activity4.70E-04
15GO:0042834: peptidoglycan binding4.70E-04
16GO:0008676: 3-deoxy-8-phosphooctulonate synthase activity4.70E-04
17GO:0004645: phosphorylase activity4.70E-04
18GO:0050308: sugar-phosphatase activity4.70E-04
19GO:0019203: carbohydrate phosphatase activity4.70E-04
20GO:0008395: steroid hydroxylase activity4.70E-04
21GO:0005080: protein kinase C binding4.70E-04
22GO:0008242: omega peptidase activity4.70E-04
23GO:0030785: [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity4.70E-04
24GO:0042586: peptide deformylase activity4.70E-04
25GO:0052381: tRNA dimethylallyltransferase activity4.70E-04
26GO:0010313: phytochrome binding4.70E-04
27GO:0000170: sphingosine hydroxylase activity4.70E-04
28GO:0050139: nicotinate-N-glucosyltransferase activity4.70E-04
29GO:0004425: indole-3-glycerol-phosphate synthase activity4.70E-04
30GO:1905201: gibberellin transmembrane transporter activity4.70E-04
31GO:0008184: glycogen phosphorylase activity4.70E-04
32GO:0004856: xylulokinase activity4.70E-04
33GO:0047134: protein-disulfide reductase activity5.69E-04
34GO:0004791: thioredoxin-disulfide reductase activity7.60E-04
35GO:0042284: sphingolipid delta-4 desaturase activity1.01E-03
36GO:0034722: gamma-glutamyl-peptidase activity1.01E-03
37GO:0008493: tetracycline transporter activity1.01E-03
38GO:0004826: phenylalanine-tRNA ligase activity1.01E-03
39GO:0017118: lipoyltransferase activity1.01E-03
40GO:0003852: 2-isopropylmalate synthase activity1.01E-03
41GO:0004817: cysteine-tRNA ligase activity1.01E-03
42GO:0016671: oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor1.06E-03
43GO:0003913: DNA photolyase activity1.65E-03
44GO:0002161: aminoacyl-tRNA editing activity1.65E-03
45GO:0004148: dihydrolipoyl dehydrogenase activity1.65E-03
46GO:0016805: dipeptidase activity1.65E-03
47GO:0015462: ATPase-coupled protein transmembrane transporter activity1.65E-03
48GO:0004180: carboxypeptidase activity1.65E-03
49GO:0015238: drug transmembrane transporter activity2.15E-03
50GO:0009041: uridylate kinase activity2.39E-03
51GO:0052656: L-isoleucine transaminase activity2.39E-03
52GO:0052654: L-leucine transaminase activity2.39E-03
53GO:0052655: L-valine transaminase activity2.39E-03
54GO:0005215: transporter activity3.10E-03
55GO:0004084: branched-chain-amino-acid transaminase activity3.22E-03
56GO:0046556: alpha-L-arabinofuranosidase activity3.22E-03
57GO:0004335: galactokinase activity3.22E-03
58GO:0004659: prenyltransferase activity3.22E-03
59GO:0004176: ATP-dependent peptidase activity3.34E-03
60GO:0016773: phosphotransferase activity, alcohol group as acceptor4.13E-03
61GO:0016208: AMP binding5.11E-03
62GO:0035673: oligopeptide transmembrane transporter activity5.11E-03
63GO:0102229: amylopectin maltohydrolase activity5.11E-03
64GO:0003968: RNA-directed 5'-3' RNA polymerase activity5.11E-03
65GO:2001070: starch binding5.11E-03
66GO:0080030: methyl indole-3-acetate esterase activity5.11E-03
67GO:1990714: hydroxyproline O-galactosyltransferase activity5.11E-03
68GO:0004526: ribonuclease P activity5.11E-03
69GO:0045156: electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity6.17E-03
70GO:0016832: aldehyde-lyase activity6.17E-03
71GO:0016161: beta-amylase activity6.17E-03
72GO:0004723: calcium-dependent protein serine/threonine phosphatase activity6.17E-03
73GO:0008195: phosphatidate phosphatase activity6.17E-03
74GO:0004519: endonuclease activity6.58E-03
75GO:0004033: aldo-keto reductase (NADP) activity8.49E-03
76GO:0008237: metallopeptidase activity8.76E-03
77GO:0015035: protein disulfide oxidoreductase activity9.03E-03
78GO:0008173: RNA methyltransferase activity9.75E-03
79GO:0008889: glycerophosphodiester phosphodiesterase activity1.11E-02
80GO:0071949: FAD binding1.11E-02
81GO:0008138: protein tyrosine/serine/threonine phosphatase activity1.11E-02
82GO:0009815: 1-aminocyclopropane-1-carboxylate oxidase activity1.11E-02
83GO:0102483: scopolin beta-glucosidase activity1.16E-02
84GO:0004805: trehalose-phosphatase activity1.39E-02
85GO:0030234: enzyme regulator activity1.39E-02
86GO:0008047: enzyme activator activity1.39E-02
87GO:0015020: glucuronosyltransferase activity1.39E-02
88GO:0016614: oxidoreductase activity, acting on CH-OH group of donors1.49E-02
89GO:0008515: sucrose transmembrane transporter activity1.54E-02
90GO:0008559: xenobiotic-transporting ATPase activity1.54E-02
91GO:0044183: protein binding involved in protein folding1.54E-02
92GO:0004675: transmembrane receptor protein serine/threonine kinase activity1.60E-02
93GO:0015297: antiporter activity1.65E-02
94GO:0000049: tRNA binding1.70E-02
95GO:0015198: oligopeptide transporter activity1.70E-02
96GO:0008422: beta-glucosidase activity1.79E-02
97GO:0000149: SNARE binding1.79E-02
98GO:0004089: carbonate dehydratase activity1.86E-02
99GO:0019888: protein phosphatase regulator activity1.86E-02
100GO:0005484: SNAP receptor activity2.12E-02
101GO:0008146: sulfotransferase activity2.20E-02
102GO:0051119: sugar transmembrane transporter activity2.20E-02
103GO:0102337: 3-oxo-cerotoyl-CoA synthase activity2.38E-02
104GO:0102338: 3-oxo-lignoceronyl-CoA synthase activity2.38E-02
105GO:0102336: 3-oxo-arachidoyl-CoA synthase activity2.38E-02
106GO:0031418: L-ascorbic acid binding2.56E-02
107GO:0005528: FK506 binding2.56E-02
108GO:0005345: purine nucleobase transmembrane transporter activity2.74E-02
109GO:0033612: receptor serine/threonine kinase binding2.94E-02
110GO:0003964: RNA-directed DNA polymerase activity2.94E-02
111GO:0003727: single-stranded RNA binding3.54E-02
112GO:0008514: organic anion transmembrane transporter activity3.54E-02
113GO:0050660: flavin adenine dinucleotide binding3.63E-02
114GO:0004812: aminoacyl-tRNA ligase activity3.74E-02
115GO:0016874: ligase activity3.82E-02
116GO:0008080: N-acetyltransferase activity4.17E-02
117GO:0004386: helicase activity4.42E-02
118GO:0001135: transcription factor activity, RNA polymerase II transcription factor recruiting4.92E-02
RankGO TermAdjusted P value
1GO:0009507: chloroplast1.55E-09
2GO:0009508: plastid chromosome5.95E-06
3GO:0009295: nucleoid1.15E-05
4GO:0009570: chloroplast stroma1.97E-05
5GO:0000427: plastid-encoded plastid RNA polymerase complex1.01E-03
6GO:0009706: chloroplast inner membrane1.75E-03
7GO:0009654: photosystem II oxygen evolving complex3.04E-03
8GO:0009544: chloroplast ATP synthase complex3.22E-03
9GO:0019898: extrinsic component of membrane6.34E-03
10GO:0048226: Casparian strip8.49E-03
11GO:0012507: ER to Golgi transport vesicle membrane8.49E-03
12GO:0009501: amyloplast8.49E-03
13GO:0009941: chloroplast envelope8.70E-03
14GO:0031969: chloroplast membrane1.10E-02
15GO:0010494: cytoplasmic stress granule1.11E-02
16GO:0010598: NAD(P)H dehydrogenase complex (plastoquinone)1.11E-02
17GO:0000159: protein phosphatase type 2A complex1.54E-02
18GO:0009535: chloroplast thylakoid membrane1.61E-02
19GO:0005578: proteinaceous extracellular matrix1.86E-02
20GO:0031902: late endosome membrane1.95E-02
21GO:0031201: SNARE complex1.95E-02
22GO:0030095: chloroplast photosystem II2.03E-02
23GO:0009534: chloroplast thylakoid2.13E-02
24GO:0043231: intracellular membrane-bounded organelle2.28E-02
25GO:0009536: plastid2.82E-02
26GO:0005770: late endosome4.17E-02
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Gene type



Gene DE type