co-expression network

GO Enrichment Analysis of Co-expressed Genes with

AT3G54460

GO-BP

GO-MF

GO-CC

Rank	GO Term	Adjusted P value
1	GO:2000042: negative regulation of double-strand break repair via homologous recombination	0.00E+00
2	GO:0042407: cristae formation	0.00E+00
3	GO:0018023: peptidyl-lysine trimethylation	0.00E+00
4	GO:0015805: S-adenosyl-L-methionine transport	0.00E+00
5	GO:0031222: arabinan catabolic process	0.00E+00
6	GO:0042352: GDP-L-fucose salvage	0.00E+00
7	GO:0061157: mRNA destabilization	0.00E+00
8	GO:0002184: cytoplasmic translational termination	0.00E+00
9	GO:0043392: negative regulation of DNA binding	0.00E+00
10	GO:0046838: phosphorylated carbohydrate dephosphorylation	0.00E+00
11	GO:0005983: starch catabolic process	2.47E-08
12	GO:0018026: peptidyl-lysine monomethylation	5.37E-06
13	GO:2000012: regulation of auxin polar transport	7.45E-05
14	GO:0042793: transcription from plastid promoter	1.68E-04
15	GO:2000033: regulation of seed dormancy process	2.28E-04
16	GO:0046520: sphingoid biosynthetic process	3.44E-04
17	GO:0010480: microsporocyte differentiation	3.44E-04
18	GO:0043686: co-translational protein modification	3.44E-04
19	GO:0043007: maintenance of rDNA	3.44E-04
20	GO:0015904: tetracycline transport	3.44E-04
21	GO:0000023: maltose metabolic process	3.44E-04
22	GO:0000025: maltose catabolic process	3.44E-04
23	GO:0005980: glycogen catabolic process	3.44E-04
24	GO:0030198: extracellular matrix organization	3.44E-04
25	GO:0006353: DNA-templated transcription, termination	3.72E-04
26	GO:0005975: carbohydrate metabolic process	7.25E-04
27	GO:0006423: cysteinyl-tRNA aminoacylation	7.51E-04
28	GO:0009629: response to gravity	7.51E-04
29	GO:0019388: galactose catabolic process	7.51E-04
30	GO:0007154: cell communication	7.51E-04
31	GO:0071497: cellular response to freezing	7.51E-04
32	GO:0031648: protein destabilization	7.51E-04
33	GO:0006568: tryptophan metabolic process	7.51E-04
34	GO:0071452: cellular response to singlet oxygen	7.51E-04
35	GO:0010027: thylakoid membrane organization	8.08E-04
36	GO:0009658: chloroplast organization	8.64E-04
37	GO:0009773: photosynthetic electron transport in photosystem I	8.68E-04
38	GO:0006006: glucose metabolic process	1.12E-03
39	GO:0010588: cotyledon vascular tissue pattern formation	1.12E-03
40	GO:0033591: response to L-ascorbic acid	1.21E-03
41	GO:0046739: transport of virus in multicellular host	1.75E-03
42	GO:0009590: detection of gravity	1.75E-03
43	GO:0009102: biotin biosynthetic process	1.75E-03
44	GO:0043433: negative regulation of sequence-specific DNA binding transcription factor activity	1.75E-03
45	GO:0009640: photomorphogenesis	2.09E-03
46	GO:0009793: embryo development ending in seed dormancy	2.15E-03
47	GO:1902347: response to strigolactone	2.35E-03
48	GO:0006808: regulation of nitrogen utilization	2.35E-03
49	GO:1901141: regulation of lignin biosynthetic process	2.35E-03
50	GO:0042274: ribosomal small subunit biogenesis	2.35E-03
51	GO:0022622: root system development	2.35E-03
52	GO:0006221: pyrimidine nucleotide biosynthetic process	2.35E-03
53	GO:0016042: lipid catabolic process	2.37E-03
54	GO:0031365: N-terminal protein amino acid modification	3.00E-03
55	GO:0006662: glycerol ether metabolic process	3.45E-03
56	GO:0009741: response to brassinosteroid	3.45E-03
57	GO:0018258: protein O-linked glycosylation via hydroxyproline	3.71E-03
58	GO:1902456: regulation of stomatal opening	3.71E-03
59	GO:0010405: arabinogalactan protein metabolic process	3.71E-03
60	GO:0019288: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	3.71E-03
61	GO:0009959: negative gravitropism	3.71E-03
62	GO:0019252: starch biosynthetic process	3.98E-03
63	GO:0006508: proteolysis	4.44E-03
64	GO:0042026: protein refolding	4.47E-03
65	GO:0042372: phylloquinone biosynthetic process	4.47E-03
66	GO:0006458: 'de novo' protein folding	4.47E-03
67	GO:0048509: regulation of meristem development	4.47E-03
68	GO:0030488: tRNA methylation	4.47E-03
69	GO:1901657: glycosyl compound metabolic process	4.85E-03
70	GO:0009742: brassinosteroid mediated signaling pathway	5.17E-03
71	GO:0010098: suspensor development	5.27E-03
72	GO:0030307: positive regulation of cell growth	5.27E-03
73	GO:0032880: regulation of protein localization	5.27E-03
74	GO:0010161: red light signaling pathway	5.27E-03
75	GO:0048437: floral organ development	5.27E-03
76	GO:0009642: response to light intensity	6.13E-03
77	GO:0042255: ribosome assembly	6.13E-03
78	GO:0046620: regulation of organ growth	6.13E-03
79	GO:0000105: histidine biosynthetic process	6.13E-03
80	GO:0005978: glycogen biosynthetic process	6.13E-03
81	GO:0009416: response to light stimulus	6.83E-03
82	GO:0010497: plasmodesmata-mediated intercellular transport	7.03E-03
83	GO:0009657: plastid organization	7.03E-03
84	GO:0010100: negative regulation of photomorphogenesis	7.03E-03
85	GO:0006526: arginine biosynthetic process	7.03E-03
86	GO:0032544: plastid translation	7.03E-03
87	GO:0010099: regulation of photomorphogenesis	7.03E-03
88	GO:0009790: embryo development	7.78E-03
89	GO:0051865: protein autoubiquitination	7.97E-03
90	GO:0010206: photosystem II repair	7.97E-03
91	GO:0006783: heme biosynthetic process	7.97E-03
92	GO:0009817: defense response to fungus, incompatible interaction	8.05E-03
93	GO:0000160: phosphorelay signal transduction system	8.47E-03
94	GO:0006633: fatty acid biosynthetic process	8.55E-03
95	GO:0031425: chloroplast RNA processing	8.96E-03
96	GO:0005982: starch metabolic process	8.96E-03
97	GO:0009638: phototropism	8.96E-03
98	GO:0043067: regulation of programmed cell death	8.96E-03
99	GO:0009098: leucine biosynthetic process	8.96E-03
100	GO:1900865: chloroplast RNA modification	8.96E-03
101	GO:0009451: RNA modification	9.92E-03
102	GO:0048829: root cap development	1.00E-02
103	GO:0010162: seed dormancy process	1.00E-02
104	GO:0034599: cellular response to oxidative stress	1.07E-02
105	GO:0009073: aromatic amino acid family biosynthetic process	1.11E-02
106	GO:0048229: gametophyte development	1.11E-02
107	GO:0010015: root morphogenesis	1.11E-02
108	GO:0012501: programmed cell death	1.22E-02
109	GO:0010102: lateral root morphogenesis	1.33E-02
110	GO:0010628: positive regulation of gene expression	1.33E-02
111	GO:0010075: regulation of meristem growth	1.33E-02
112	GO:0009767: photosynthetic electron transport chain	1.33E-02
113	GO:0010020: chloroplast fission	1.45E-02
114	GO:0009266: response to temperature stimulus	1.45E-02
115	GO:0009934: regulation of meristem structural organization	1.45E-02
116	GO:0090351: seedling development	1.58E-02
117	GO:0080188: RNA-directed DNA methylation	1.58E-02
118	GO:0009734: auxin-activated signaling pathway	1.63E-02
119	GO:0000162: tryptophan biosynthetic process	1.70E-02
120	GO:0009736: cytokinin-activated signaling pathway	1.79E-02
121	GO:0010187: negative regulation of seed germination	1.83E-02
122	GO:0003333: amino acid transmembrane transport	2.10E-02
123	GO:0048511: rhythmic process	2.10E-02
124	GO:0061077: chaperone-mediated protein folding	2.10E-02
125	GO:0048278: vesicle docking	2.10E-02
126	GO:0048367: shoot system development	2.18E-02
127	GO:2000022: regulation of jasmonic acid mediated signaling pathway	2.24E-02
128	GO:0031348: negative regulation of defense response	2.24E-02
129	GO:0007169: transmembrane receptor protein tyrosine kinase signaling pathway	2.30E-02
130	GO:0009686: gibberellin biosynthetic process	2.38E-02
131	GO:0009740: gibberellic acid mediated signaling pathway	2.40E-02
132	GO:0009624: response to nematode	2.55E-02
133	GO:0030154: cell differentiation	2.66E-02
134	GO:0008284: positive regulation of cell proliferation	2.68E-02
135	GO:0009733: response to auxin	2.80E-02
136	GO:0080022: primary root development	2.83E-02
137	GO:0010087: phloem or xylem histogenesis	2.83E-02
138	GO:0010118: stomatal movement	2.83E-02
139	GO:0048653: anther development	2.83E-02
140	GO:0009958: positive gravitropism	2.99E-02
141	GO:0010305: leaf vascular tissue pattern formation	2.99E-02
142	GO:0006520: cellular amino acid metabolic process	2.99E-02
143	GO:0010197: polar nucleus fusion	2.99E-02
144	GO:0010182: sugar mediated signaling pathway	2.99E-02
145	GO:0009960: endosperm development	2.99E-02
146	GO:0048544: recognition of pollen	3.15E-02
147	GO:0061025: membrane fusion	3.15E-02
148	GO:0042752: regulation of circadian rhythm	3.15E-02
149	GO:0009058: biosynthetic process	3.36E-02
150	GO:0048510: regulation of timing of transition from vegetative to reproductive phase	3.47E-02
151	GO:0071554: cell wall organization or biogenesis	3.47E-02
152	GO:0010583: response to cyclopentenone	3.64E-02
153	GO:0030163: protein catabolic process	3.81E-02
154	GO:0010252: auxin homeostasis	3.98E-02
155	GO:0010029: regulation of seed germination	4.69E-02
156	GO:0009607: response to biotic stimulus	4.69E-02
157	GO:0006906: vesicle fusion	4.87E-02
158	GO:0006470: protein dephosphorylation	5.00E-02

Rank	GO Term	Adjusted P value
1	GO:0050518: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	0.00E+00
2	GO:0051060: pullulanase activity	0.00E+00
3	GO:0071633: dihydroceramidase activity	0.00E+00
4	GO:0047661: amino-acid racemase activity	0.00E+00
5	GO:0008756: o-succinylbenzoate-CoA ligase activity	0.00E+00
6	GO:0003949: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity	0.00E+00
7	GO:0097100: supercoiled DNA binding	0.00E+00
8	GO:0005201: extracellular matrix structural constituent	0.00E+00
9	GO:0047341: fucose-1-phosphate guanylyltransferase activity	0.00E+00
10	GO:0004076: biotin synthase activity	0.00E+00
11	GO:0047450: crotonoyl-[acyl-carrier-protein] hydratase activity	0.00E+00
12	GO:0005363: maltose transmembrane transporter activity	0.00E+00
13	GO:0090711: FMN hydrolase activity	0.00E+00
14	GO:0010303: limit dextrinase activity	0.00E+00
15	GO:0051752: phosphoglucan, water dikinase activity	0.00E+00
16	GO:0050201: fucokinase activity	0.00E+00
17	GO:0016279: protein-lysine N-methyltransferase activity	7.42E-05
18	GO:2001070: starch binding	1.68E-04
19	GO:0042586: peptide deformylase activity	3.44E-04
20	GO:0004856: xylulokinase activity	3.44E-04
21	GO:0010313: phytochrome binding	3.44E-04
22	GO:0004134: 4-alpha-glucanotransferase activity	3.44E-04
23	GO:0004645: phosphorylase activity	3.44E-04
24	GO:0009374: biotin binding	3.44E-04
25	GO:0019203: carbohydrate phosphatase activity	3.44E-04
26	GO:0030785: [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity	3.44E-04
27	GO:0003942: N-acetyl-gamma-glutamyl-phosphate reductase activity	3.44E-04
28	GO:0000170: sphingosine hydroxylase activity	3.44E-04
29	GO:0050139: nicotinate-N-glucosyltransferase activity	3.44E-04
30	GO:0004425: indole-3-glycerol-phosphate synthase activity	3.44E-04
31	GO:0008184: glycogen phosphorylase activity	3.44E-04
32	GO:0050308: sugar-phosphatase activity	3.44E-04
33	GO:0008493: tetracycline transporter activity	7.51E-04
34	GO:0019171: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity	7.51E-04
35	GO:0004614: phosphoglucomutase activity	7.51E-04
36	GO:0019200: carbohydrate kinase activity	7.51E-04
37	GO:0003852: 2-isopropylmalate synthase activity	7.51E-04
38	GO:0004817: cysteine-tRNA ligase activity	7.51E-04
39	GO:0000095: S-adenosyl-L-methionine transmembrane transporter activity	7.51E-04
40	GO:0042284: sphingolipid delta-4 desaturase activity	7.51E-04
41	GO:0005504: fatty acid binding	1.21E-03
42	GO:0016620: oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	1.21E-03
43	GO:0017150: tRNA dihydrouridine synthase activity	1.21E-03
44	GO:0009041: uridylate kinase activity	1.75E-03
45	GO:0043023: ribosomal large subunit binding	1.75E-03
46	GO:0004176: ATP-dependent peptidase activity	2.11E-03
47	GO:0043621: protein self-association	2.31E-03
48	GO:0045430: chalcone isomerase activity	2.35E-03
49	GO:0046556: alpha-L-arabinofuranosidase activity	2.35E-03
50	GO:0004335: galactokinase activity	2.35E-03
51	GO:0003727: single-stranded RNA binding	2.74E-03
52	GO:0047134: protein-disulfide reductase activity	2.96E-03
53	GO:0016773: phosphotransferase activity, alcohol group as acceptor	3.00E-03
54	GO:0003989: acetyl-CoA carboxylase activity	3.00E-03
55	GO:0003824: catalytic activity	3.09E-03
56	GO:0001085: RNA polymerase II transcription factor binding	3.45E-03
57	GO:0004556: alpha-amylase activity	3.71E-03
58	GO:0016208: AMP binding	3.71E-03
59	GO:0004791: thioredoxin-disulfide reductase activity	3.71E-03
60	GO:1990714: hydroxyproline O-galactosyltransferase activity	3.71E-03
61	GO:0004723: calcium-dependent protein serine/threonine phosphatase activity	4.47E-03
62	GO:0045156: electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity	4.47E-03
63	GO:0000156: phosphorelay response regulator activity	4.85E-03
64	GO:0016671: oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	4.85E-03
65	GO:0008237: metallopeptidase activity	5.49E-03
66	GO:0008173: RNA methyltransferase activity	7.03E-03
67	GO:0102483: scopolin beta-glucosidase activity	7.26E-03
68	GO:0008138: protein tyrosine/serine/threonine phosphatase activity	7.97E-03
69	GO:0001228: transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding	9.32E-03
70	GO:0004519: endonuclease activity	1.11E-02
71	GO:0044183: protein binding involved in protein folding	1.11E-02
72	GO:0047372: acylglycerol lipase activity	1.11E-02
73	GO:0008422: beta-glucosidase activity	1.12E-02
74	GO:0031072: heat shock protein binding	1.33E-02
75	GO:0008083: growth factor activity	1.45E-02
76	GO:0004190: aspartic-type endopeptidase activity	1.58E-02
77	GO:0008168: methyltransferase activity	1.60E-02
78	GO:0000287: magnesium ion binding	1.64E-02
79	GO:0005528: FK506 binding	1.83E-02
80	GO:0016298: lipase activity	1.85E-02
81	GO:0033612: receptor serine/threonine kinase binding	2.10E-02
82	GO:0052689: carboxylic ester hydrolase activity	2.50E-02
83	GO:0051082: unfolded protein binding	2.55E-02
84	GO:0015035: protein disulfide oxidoreductase activity	2.62E-02
85	GO:0004252: serine-type endopeptidase activity	3.54E-02
86	GO:0000977: RNA polymerase II regulatory region sequence-specific DNA binding	3.63E-02
87	GO:0005507: copper ion binding	3.86E-02
88	GO:0016759: cellulose synthase activity	3.98E-02
89	GO:0016413: O-acetyltransferase activity	4.33E-02

Rank	GO Term	Adjusted P value
1	GO:0009507: chloroplast	1.47E-11
2	GO:0009570: chloroplast stroma	7.66E-07
3	GO:0000427: plastid-encoded plastid RNA polymerase complex	5.37E-06
4	GO:0009295: nucleoid	6.98E-04
5	GO:0009534: chloroplast thylakoid	8.13E-04
6	GO:0009508: plastid chromosome	1.12E-03
7	GO:0009317: acetyl-CoA carboxylase complex	1.21E-03
8	GO:0019897: extrinsic component of plasma membrane	1.21E-03
9	GO:0009536: plastid	1.29E-03
10	GO:0042646: plastid nucleoid	1.75E-03
11	GO:0009941: chloroplast envelope	2.22E-03
12	GO:0009544: chloroplast ATP synthase complex	2.35E-03
13	GO:0005655: nucleolar ribonuclease P complex	4.47E-03
14	GO:0009706: chloroplast inner membrane	4.80E-03
15	GO:0009501: amyloplast	6.13E-03
16	GO:0005667: transcription factor complex	6.89E-03
17	GO:0042644: chloroplast nucleoid	7.97E-03
18	GO:0010598: NAD(P)H dehydrogenase complex (plastoquinone)	7.97E-03
19	GO:0090404: pollen tube tip	1.11E-02
20	GO:0043231: intracellular membrane-bounded organelle	1.13E-02
21	GO:0005578: proteinaceous extracellular matrix	1.33E-02
22	GO:0009654: photosystem II oxygen evolving complex	1.96E-02
23	GO:0031969: chloroplast membrane	2.21E-02
24	GO:0005770: late endosome	2.99E-02
25	GO:0009543: chloroplast thylakoid lumen	3.19E-02
26	GO:0019898: extrinsic component of membrane	3.31E-02
27	GO:0005778: peroxisomal membrane	4.15E-02
28	GO:0010319: stromule	4.15E-02
29	GO:0005615: extracellular space	4.89E-02