4.0:Information of module
cop1 Seedling Dark
In comparison with aerial organ callus inducing medium 96 h help
Scatter plot of seleted modules.
Trend of Up regulated genes including module
GOID Term Ontology p-value
GO:0015979 photosynthesis BP 5.526e-83
GO:0019684 photosynthesis, light reaction BP 4.929e-75
GO:0006091 generation of precursor metabolites and ... BP 7.092e-61
･･･ ･･･ ･･･ ･･･
View Hierarchical networks of GOs (      )
Trend of Down regulated genes including module
GOID Term Ontology p-value
GO:0042221 response to chemical BP 1.792e-07
GO:0008152 metabolic process BP 2.941e-07
GO:0050896 response to stimulus BP 4.029e-07
･･･ ･･･ ･･･ ･･･
View Hierarchical networks of GOs (      )
List of genes in module
･･･up requlated genes  ･･･down regulated genes
probeID AGICode Annotation Log2 signal ratio
cop1 Seedling Dark		 Log2 signal ratio
aerial organ callus inducing medium 96 h
1 264636_at AT1G65490 unknown 1.311 -0.546
2 256497_at AT1G31580 CXC750, ECS1 1.178 -0.712
3 245025_at ATCG00130 ATPF 1.094 -0.434
4 244934_at ATCG01080 NDHG 1.045 -0.455
5 244933_at ATCG01070 NDHE 1.041 -0.433
6 256796_at AT3G22210 unknown 0.982 -0.736
7 244972_at ATCG00680 PSBB, photosystem II reaction center protein B 0.948 -0.431
8 245448_at AT4G16860 RPP4, recognition of peronospora parasitica 4 0.944 -0.292
9 266279_at AT2G29290 [NAD(P)-binding Rossmann-fold superfamily protein] 0.907 -1.076
10 266277_at AT2G29310 [NAD(P)-binding Rossmann-fold superfamily protein] 0.902 -0.168
11 244966_at ATCG00600 PETG 0.893 -0.385
12 265611_at AT2G25510 unknown 0.893 -0.488
13 248062_at AT5G55450 [Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein] 0.874 -0.424
14 248683_at AT5G48490 [Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein] 0.874 -1.287
15 245049_at ATCG00050 RPS16, ribosomal protein S16 0.870 -0.740
16 249876_at AT5G23060 CaS, calcium sensing receptor 0.821 -0.801
17 263410_at AT2G04039 unknown 0.819 -1.024
18 265699_at AT2G03550 [alpha/beta-Hydrolases superfamily protein] 0.818 -0.407
19 245026_at ATCG00140 ATPH 0.796 -0.313
20 245017_at ATCG00510 PSAI, photsystem I subunit I 0.793 -0.356
21 263034_at AT1G24020 MLP423, MLP-like protein 423 0.789 -0.332
22 255852_at AT1G66970 GDPDL1, Glycerophosphodiester phosphodiesterase (GDPD) like 1, SVL2, SHV3-like 2 0.770 -0.737
23 254794_at AT4G12970 EPFL9, STOMAGEN, STOMAGEN 0.764 -0.817
24 248839_at AT5G46690 bHLH071, beta HLH protein 71 0.753 -0.885
25 255046_at AT4G09650 ATPD, ATP synthase delta-subunit gene, PDE332, PIGMENT DEFECTIVE 332 0.737 -0.578
26 252463_at AT3G47070 [LOCATED IN: thylakoid, chloroplast thylakoid membrane, chloroplast, chloroplast envelope] 0.735 -0.592
27 245024_at ATCG00120 ATPA, ATP synthase subunit alpha 0.726 -0.291
28 245002_at ATCG00270 PSBD, photosystem II reaction center protein D 0.725 -0.434
29 254384_at AT4G21870 [HSP20-like chaperones superfamily protein] 0.724 -0.571
30 262288_at AT1G70760 CRR23, CHLORORESPIRATORY REDUCTION 23, NdhL, NADH dehydrogenase-like complex L 0.719 -1.035
31 258897_at AT3G05730 [LOCATED IN: endomembrane system] 0.714 -0.266
32 266979_at AT2G39470 PnsL1, Photosynthetic NDH subcomplex L 1, PPL2, PsbP-like protein 2 0.712 -1.099
33 264442_at AT1G27480 [alpha/beta-Hydrolases superfamily protein] 0.704 -0.902
34 262612_at AT1G14150 PnsL2, Photosynthetic NDH subcomplex L 2, PQL1, PsbQ-like 1, PQL2, PsbQ-like 2 0.699 -1.169
35 261913_at AT1G65860 FMO GS-OX1, flavin-monooxygenase glucosinolate S-oxygenase 1 0.692 -0.149
36 264201_at AT1G22630 unknown 0.691 -0.767
37 260696_at AT1G32520 unknown 0.687 -0.822
38 245505_at AT4G15690 [Thioredoxin superfamily protein] 0.680 0.271
39 260004_at AT1G67860 unknown 0.679 0.269
40 257635_at AT3G26280 CYP71B4, cytochrome P450, family 71, subfamily B, polypeptide 4 0.679 0.229
41 245008_at ATCG00360 YCF3 0.670 -0.396
42 260546_at AT2G43520 ATTI2, trypsin inhibitor protein 2, TI2, trypsin inhibitor protein 2 0.660 -0.030
43 257966_at AT3G19800 unknown 0.655 -0.700
44 262680_at AT1G75880 [SGNH hydrolase-type esterase superfamily protein] 0.641 0.444
45 261958_at AT1G64500 [Glutaredoxin family protein] 0.641 -0.554
46 247899_at AT5G57345 unknown 0.638 -0.627
47 264435_at AT1G10360 ATGSTU18, glutathione S-transferase TAU 18, GST29, GLUTATHIONE S-TRANSFERASE 29, GSTU18, glutathione S-transferase TAU 18 0.635 -0.851
48 264195_at AT1G22690 [Gibberellin-regulated family protein] 0.634 -0.008
49 256969_at AT3G21080 [ABC transporter-related] 0.626 0.424
50 249775_at AT5G24160 SQE6, squalene monoxygenase 6 0.621 -0.472
51 255807_at AT4G10270 [Wound-responsive family protein] 0.619 0.627
52 244998_at ATCG00180 RPOC1 0.616 -0.371
53 267555_at AT2G32765 ATSUMO5, SUM5, SUMO 5, SUMO5, small ubiquitinrelated modifier 5 0.616 -0.247
54 249645_at AT5G36910 THI2.2, thionin 2.2 0.609 -0.850
55 264037_at AT2G03750 [P-loop containing nucleoside triphosphate hydrolases superfamily protein] 0.608 -0.842
56 244996_at ATCG00160 RPS2, ribosomal protein S2 0.595 -0.384
57 251221_at AT3G62550 [Adenine nucleotide alpha hydrolases-like superfamily protein] 0.594 0.167
58 256336_at AT1G72030 [Acyl-CoA N-acyltransferases (NAT) superfamily protein] 0.581 -0.486
59 252876_at AT4G39970 [Haloacid dehalogenase-like hydrolase (HAD) superfamily protein] 0.581 -0.743
60 259625_at AT1G42970 GAPB, glyceraldehyde-3-phosphate dehydrogenase B subunit 0.579 -0.624
61 247362_at AT5G63140 ATPAP29, purple acid phosphatase 29, PAP29, PAP29, purple acid phosphatase 29 0.576 -0.031
62 260368_at AT1G69700 ATHVA22C, HVA22 homologue C, HVA22C, HVA22 homologue C 0.575 -0.057
63 260012_at AT1G67865 unknown 0.573 0.206
64 253966_at AT4G26520 AtFBA7, FBA7, fructose-bisphosphate aldolase 7 0.570 -0.583
65 262543_at AT1G34245 EPF2, EPIDERMAL PATTERNING FACTOR 2 0.570 -0.655
66 259773_at AT1G29500 SAUR66, SMALL AUXIN UPREGULATED RNA 66 0.566 0.007
67 245050_at ATCG00070 PSBK, photosystem II reaction center protein K precursor 0.564 -0.108
68 245003_at ATCG00280 PSBC, photosystem II reaction center protein C 0.561 -0.345
69 249932_at AT5G22390 unknown 0.558 -0.600
70 264016_at AT2G21220 SAUR12, SMALL AUXIN UPREGULATED RNA 12 0.557 -0.340
71 253943_at AT4G27030 FAD4, FATTY ACID DESATURASE 4, FADA, fatty acid desaturase A 0.551 -1.242
72 255298_at AT4G04840 ATMSRB6, methionine sulfoxide reductase B6, MSRB6, methionine sulfoxide reductase B6 0.551 -0.751
73 265569_at AT2G05620 AtPGR5, PGR5, proton gradient regulation 5 0.549 -0.468
74 252946_at AT4G39235 unknown 0.547 -0.201
75 248623_at AT5G49170 unknown 0.544 -0.196
76 252965_at AT4G38860 SAUR16, SMALL AUXIN UPREGULATED RNA 16 0.543 -0.324
77 260312_at AT1G63880 [Disease resistance protein (TIR-NBS-LRR class) family] 0.540 -0.220
78 245006_at ATCG00340 PSAB 0.540 -0.105
79 262970_at AT1G75690 LQY1, LOW QUANTUM YIELD OF PHOTOSYSTEM II 1 0.537 -0.731
80 254687_at AT4G13770 CYP83A1, cytochrome P450, family 83, subfamily A, polypeptide 1, REF2, REDUCED EPIDERMAL FLUORESCENCE 2 0.537 -0.095
81 245592_at AT4G14540 NF-YB3, nuclear factor Y, subunit B3 0.534 -0.446
82 260968_at AT1G12250 [Pentapeptide repeat-containing protein] 0.528 -0.639
83 251031_at AT5G02120 OHP, one helix protein, PDE335, PIGMENT DEFECTIVE 335 0.524 -0.631
84 257954_at AT3G21760 HYR1, HYPOSTATIN RESISTANCE 1 0.524 -0.580
85 250563_at AT5G08050 unknown 0.523 -0.634
86 250207_at AT5G13930 ATCHS, CHS, CHALCONE SYNTHASE, TT4, TRANSPARENT TESTA 4 0.522 -0.786
87 255331_at AT4G04330 AtRbcX1, RbcX1, homologue of cyanobacterial RbcX 1 0.520 -0.650
88 250073_at AT5G17170 ENH1, enhancer of sos3-1 0.518 -0.690
89 260877_at AT1G21500 unknown 0.514 -0.877
90 260542_at AT2G43560 [FKBP-like peptidyl-prolyl cis-trans isomerase family protein] 0.514 -0.738
91 251826_at AT3G55110 ABCG18, ATP-binding cassette G18 0.511 -0.472
92 251885_at AT3G54050 HCEF1, high cyclic electron flow 1 0.506 -0.726
93 259460_at AT1G44000 unknown 0.505 -0.651
94 253627_at AT4G30650 [Low temperature and salt responsive protein family] 0.503 -0.028
95 251784_at AT3G55330 PPL1, PsbP-like protein 1 0.500 -0.834
96 253790_at AT4G28660 PSB28, photosystem II reaction center PSB28 protein 0.499 -0.759
97 254505_at AT4G19985 [Acyl-CoA N-acyltransferases (NAT) superfamily protein] 0.498 -0.601
98 258087_at AT3G26060 ATPRX Q, PRXQ, peroxiredoxin Q 0.496 -0.596
99 249996_at AT5G18600 [Thioredoxin superfamily protein] 0.495 0.095
100 260704_at AT1G32470 [Single hybrid motif superfamily protein] 0.492 -0.534
101 247853_at AT5G58140 NPL1, NON PHOTOTROPIC HYPOCOTYL 1-LIKE, PHOT2, phototropin 2 0.491 -0.682
102 251157_at AT3G63140 CSP41A, chloroplast stem-loop binding protein of 41 kDa 0.491 -0.894
103 257163_at AT3G24310 ATMYB71, MYB DOMAIN PROTEIN 71, MYB305, myb domain protein 305 -0.810 0.097
104 259653_at AT1G55240 unknown -0.780 0.949
105 250031_at AT5G18240 ATMYR1, ARABIDOPSIS MYB-RELATED PROTEIN 1, MYR1, myb-related protein 1 -0.627 -0.272
106 266309_at AT2G27140 [HSP20-like chaperones superfamily protein] -0.619 0.061
107 245258_at AT4G15340 04C11, ATPEN1, pentacyclic triterpene synthase 1, PEN1, pentacyclic triterpene synthase 1 -0.594 0.026
108 250302_at AT5G11920 AtcwINV6, 6-&1-fructan exohydrolase, cwINV6, 6-&1-fructan exohydrolase -0.496 0.262
109 264404_at AT2G25160 CYP82F1, cytochrome P450, family 82, subfamily F, polypeptide 1 -0.477 -0.130
110 265119_at AT1G62570 FMO GS-OX4, flavin-monooxygenase glucosinolate S-oxygenase 4 -0.476 0.458
111 263402_at AT2G04050 [MATE efflux family protein] -0.473 -0.007
112 266327_at AT2G46680 ATHB-7, homeobox 7, ATHB7, ARABIDOPSIS THALIANA HOMEOBOX 7, HB-7, homeobox 7 -0.457 0.092
113 248254_at AT5G53320 [Leucine-rich repeat protein kinase family protein] -0.447 0.633
114 246825_at AT5G26260 [TRAF-like family protein] -0.446 0.346
115 262671_at AT1G76040 CPK29, calcium-dependent protein kinase 29 -0.431 0.274
116 259897_at AT1G71380 ATCEL3, cellulase 3, ATGH9B3, ARABIDOPSIS THALIANA GLYCOSYL HYDROLASE 9B3, CEL3, cellulase 3 -0.429 0.811
117 255150_at AT4G08160 [glycosyl hydrolase family 10 protein / carbohydrate-binding domain-containing protein] -0.413 -0.006
118 261224_at AT1G20160 ATSBT5.2 -0.411 -0.160
119 246093_at AT5G20550 [2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein] -0.403 0.794
120 267311_at AT2G34670 unknown -0.402 0.163
121 251298_at AT3G62040 [Haloacid dehalogenase-like hydrolase (HAD) superfamily protein] -0.398 -0.854
122 246536_at AT5G15920 EMB2782, EMBRYO DEFECTIVE 2782, SMC5, structural maintenance of chromosomes 5 -0.397 -0.012
123 265359_at AT2G16720 ATMYB7, ARABIDOPSIS THALIANA MYB DOMAIN PROTEIN 7, ATY49, MYB7, myb domain protein 7 -0.392 0.202
124 251035_at AT5G02220 SMR4, SIAMESE-RELATED 4 -0.390 0.171
125 248736_at AT5G48110 [Terpenoid cyclases/Protein prenyltransferases superfamily protein] -0.389 0.056
126 266752_at AT2G47000 ABCB4, ATP-binding cassette B4, AtABCB4, ATPGP4, ARABIDOPSIS P-GLYCOPROTEIN 4, MDR4, MULTIDRUG RESISTANCE 4, PGP4, P-GLYCOPROTEIN 4 -0.387 0.540
127 262795_at AT1G13130 [Cellulase (glycosyl hydrolase family 5) protein] -0.386 -0.214
128 250603_at AT5G07820 [Plant calmodulin-binding protein-related] -0.375 0.263
129 261991_at AT1G33700 [Beta-glucosidase, GBA2 type family protein] -0.374 0.015
130 253842_at AT4G27860 MEB1, MEMBRANE OF ER BODY 1 -0.374 0.074
131 249045_at AT5G44380 [FAD-binding Berberine family protein] -0.370 0.881
132 254632_at AT4G18630 unknown -0.365 0.139
133 260097_at AT1G73220 AtOCT1, organic cation/carnitine transporter1, OCT1, organic cation/carnitine transporter1 -0.365 0.044
134 245436_at AT4G16620 UMAMIT8, Usually multiple acids move in and out Transporters 8 -0.362 0.488
135 251478_at AT3G59690 IQD13, IQ-domain 13 -0.361 -0.073
136 250756_at AT5G05940 ATROPGEF5, ROP GUANINE NUCLEOTIDE EXCHANGE FACTOR 5, ROPGEF5, ROP (rho of plants) guanine nucleotide exchange factor 5 -0.360 0.283
137 262873_at AT1G64700 unknown -0.359 0.310
138 261031_at AT1G17360 unknown -0.356 -0.359
139 259297_at AT3G05360 AtRLP30, receptor like protein 30, RLP30, receptor like protein 30 -0.355 0.329
140 253977_at AT4G26630 [DEK domain-containing chromatin associated protein] -0.355 -0.054
141 266688_at AT2G19660 [Cysteine/Histidine-rich C1 domain family protein] -0.351 -0.368
142 248150_at AT5G54670 ATK3, kinesin 3, KATC, KINESIN-LIKE PROTEIN IN ARABIDOPSIS THALIANA C -0.348 0.144
143 245864_at AT1G58070 unknown -0.345 -0.312
144 263629_at AT2G04850 [Auxin-responsive family protein] -0.334 -0.230
145 261491_at AT1G14350 AtMYB124, myb domain protein 124, FLP, FOUR LIPS, MYB124 -0.332 -0.002
146 262454_at AT1G11190 BFN1, bifunctional nuclease i, ENDO1, ENDONUCLEASE 1 -0.330 0.452
147 261500_at AT1G28400 unknown -0.330 0.181
148 245970_at AT5G20710 BGAL7, beta-galactosidase 7 -0.327 0.102
149 252319_at AT3G48710 [DEK domain-containing chromatin associated protein] -0.325 0.040
150 258037_at AT3G21230 4CL5, 4-coumarate:CoA ligase 5 -0.323 -0.031
151 248731_at AT5G48060 [C2 calcium/lipid-binding plant phosphoribosyltransferase family protein] -0.323 -0.127
152 262930_at AT1G65690 [Late embryogenesis abundant (LEA) hydroxyproline-rich glycoprotein family] -0.322 0.625
153 261879_at AT1G50520 CYP705A27, cytochrome P450, family 705, subfamily A, polypeptide 27 -0.319 0.177
154 247668_at AT5G60100 APRR3, pseudo-response regulator 3, PRR3, pseudo-response regulator 3 -0.319 0.113
155 253458_at AT4G32070 Phox4, Phox4 -0.319 0.219
156 251668_at AT3G57010 [Calcium-dependent phosphotriesterase superfamily protein] -0.315 0.129
157 248070_at AT5G55660 [DEK domain-containing chromatin associated protein] -0.315 0.008
158 257978_at AT3G20860 ATNEK5, NIMA-related kinase 5, NEK5, NIMA-related kinase 5 -0.314 -0.012
159 255007_at AT4G10020 AtHSD5, hydroxysteroid dehydrogenase 5, HSD5, hydroxysteroid dehydrogenase 5 -0.313 0.028
160 257534_at AT3G09670 [Tudor/PWWP/MBT superfamily protein] -0.307 -0.016
161 252958_at AT4G38620 ATMYB4, myb domain protein 4, MYB4, myb domain protein 4 -0.304 -0.102
162 265083_at AT1G03820 unknown -0.302 0.225
163 255614_at AT4G01280 [Homeodomain-like superfamily protein] -0.300 -0.118
164 249378_at AT5G40450 unknown -0.295 -0.102
165 249308_at AT5G41350 [RING/U-box superfamily protein] -0.295 0.077
166 255127_at AT4G08300 UMAMIT17, Usually multiple acids move in and out Transporters 17 -0.294 0.069
167 251967_at AT3G53390 [Transducin/WD40 repeat-like superfamily protein] -0.293 -0.011
168 253500_at AT4G31920 ARR10, response regulator 10, RR10, response regulator 10 -0.291 0.174
169 249939_at AT5G22430 [Pollen Ole e 1 allergen and extensin family protein] -0.290 0.602
170 265728_at AT2G31990 [Exostosin family protein] -0.287 0.165
171 264941_at AT1G60680 [NAD(P)-linked oxidoreductase superfamily protein] -0.286 -0.126
172 267488_at AT2G19110 ATHMA4, ARABIDOPSIS HEAVY METAL ATPASE 4, HMA4, heavy metal atpase 4 -0.284 -0.058
173 259367_at AT1G69070 unknown -0.283 0.039
174 258836_at AT3G07210 unknown -0.282 -0.054
175 246995_at AT5G67470 ATFH6, ARABIDOPSIS FORMIN HOMOLOG 6, FH6, formin homolog 6 -0.280 0.104
176 245302_at AT4G17695 KAN3, KANADI 3 -0.279 -0.095
177 247755_at AT5G59090 ATSBT4.12, subtilase 4.12, SBT4.12, subtilase 4.12 -0.275 0.259
178 246826_at AT5G26310 UGT72E3 -0.274 0.040
179 250820_at AT5G05160 RUL1, REDUCED IN LATERAL GROWTH1 -0.273 0.185
180 251061_at AT5G01830 SAUR21, SMALL AUXIN UP RNA 21 -0.272 0.200
181 263253_at AT2G31370 [Basic-leucine zipper (bZIP) transcription factor family protein] -0.271 0.016
182 261436_at AT1G07870 [Protein kinase superfamily protein] -0.271 0.235
183 267467_at AT2G30580 BMI1A, DRIP2, DREB2A-interacting protein 2 -0.270 -0.042
184 257896_at AT3G16920 ATCTL2, CTL2, chitinase-like protein 2 -0.269 -0.259
185 264527_at AT1G30760 [FAD-binding Berberine family protein] -0.268 1.226
186 257217_at AT3G14940 ATPPC3, phosphoenolpyruvate carboxylase 3, PPC3, phosphoenolpyruvate carboxylase 3 -0.266 0.190
187 250103_at AT5G16600 AtMYB43, myb domain protein 43, MYB43, myb domain protein 43 -0.265 -0.071
188 255149_at AT4G08150 BP, BREVIPEDICELLUS, BP1, BREVIPEDICELLUS 1, KNAT1, KNOTTED-like from Arabidopsis thaliana -0.265 -0.263
189 250666_at AT5G07100 WRKY26, WRKY DNA-binding protein 26 -0.264 0.761
190 252488_at AT3G46700 [UDP-Glycosyltransferase superfamily protein] -0.264 0.375
191 247312_at AT5G63970 RGLG3, RING DOMAIN LIGASE 3 -0.263 0.484
192 258828_at AT3G07130 ATPAP15, PURPLE ACID PHOSPHATASE 15, PAP15, purple acid phosphatase 15 -0.260 0.127
193 252667_at AT3G44200 ATNEK6, NIMA-RELATED KINASE6, IBO1, NEK6, NIMA (never in mitosis, gene A)-related 6 -0.260 -0.078
194 246858_at AT5G25930 [Protein kinase family protein with leucine-rich repeat domain] -0.259 0.370
195 251477_at AT3G59680 unknown -0.258 -0.155
196 252770_at AT3G42860 [zinc knuckle (CCHC-type) family protein] -0.257 0.122
197 257467_at AT1G31320 LBD4, LOB domain-containing protein 4 -0.256 0.224
198 253263_at AT4G34000 ABF3, abscisic acid responsive elements-binding factor 3, AtABF3, DPBF5, DC3 PROMOTER-BINDING FACTOR 5 -0.255 0.031
199 266795_at AT2G03070 MED8, mediator subunit 8 -0.253 -0.013
200 257766_at AT3G23030 IAA2, indole-3-acetic acid inducible 2 -0.252 0.147
201 248998_at AT5G45320 unknown -0.249 -0.004
202 254964_at AT4G11080 3xHMG-box1, 3xHigh Mobility Group-box1 -0.248 -0.074
203 253483_at AT4G31910 BAT1, BR-related AcylTransferase1, PIZ, PIZZA -0.245 0.102