CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM282698

Assay name Col_BRZ_rep2

GSE experiment GSE11216: Brassinazole treatment of arf2 and wild-type dark-grown seedlings

Click Gene ID to show a list of GSM assays in which the gene are specifically expressed.

Std2 GX %ile Std GX Gene ID Repr. ID Gene name Functional description O.I. C.G. H.G. Other DB
95.0 99.9 604.6 At4g14130 827051 XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7) xyloglucan endotransglycosylase-related protein (XTR7) O.I. C.G. H.G.
90.2 99.9 31.0 At1g27670 839659 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
84.2 99.9 71.8 At4g25580 828663 stress-responsive protein-related F:unknown;P:unknown;C:cellular_component unknown;PMOFBV O.I. C.G. H.G.
70.3 99.9 65.4 At5g57240 835830 ORP4C (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 4C) F:oxysterol binding;P:steroid metabolic process;C:cellular_component unknown;MFOP O.I. C.G. H.G.
69.1 99.9 66.1 At2g41850 818785 PGAZAT (POLYGALACTURONASE ABSCISSION ZONE A. THALIANA) ADPG2. O.I. C.G. H.G.
64.3 99.8 105.0 At3g30180 822709 BR6OX2 (BRASSINOSTEROID-6-OXIDASE 2) Encodes a cytochrome p450 enzyme that catalyzes the last reaction in the production of brassinolide. It is capable of converting 6-deoxocastasterone into castasterone, a C-6 oxidation, as well as the further conversion of castasterone into brassinolide by a Baeyer-Villinger oxidation reaction at C-6, resulting in the formation of an unusual seven-membered lactone ring. The enzyme possesses high affinity for both C28- and C27-Brassinosteroids. The expression of the gene using a CYP85A2 promoter:LUC fusion construct was shown to be under circadian and light control. O.I. C.G. H.G.
61.8 99.8 257.1 At1g10070 837543 ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2) Encodes a chloroplast branched-chain amino acid aminotransferase. Complements the yeast leu/iso-leu/val auxotrophy mutant. O.I. C.G. H.G.
54.8 99.8 98.1 At5g53980 835481 ATHB52 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 52) Encodes a homeodomain leucine zipper class I (HD-Zip I) protein. O.I. C.G. H.G.
54.7 99.8 239.0 At1g12080 837760 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA O.I. C.G. H.G.
50.9 99.8 131.6 At5g44440 834471 FAD-binding domain-containing protein F:electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity;P:unknown;C:endomembrane system;BFPOAM O.I. C.G. H.G.
48.5 99.8 107.7 At1g62770 842576 invertase/pectin methylesterase inhibitor family protein F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
48.3 99.8 228.4 At1g03090 838362 MCCA MCCA is the biotinylated subunit of the dimer MCCase, which is involved in leucine degradation. Both subunits are nuclear coded and the active enzyme is located in the mitochondrion. O.I. C.G. H.G.
47.0 99.8 173.3 At3g45300 823668 IVD (ISOVALERYL-COA-DEHYDROGENASE) Encodes isovaleryl-coenzyme a dehydrogenase. O.I. C.G. H.G.
44.8 99.8 144.2 At5g54190 835507 PORA light-dependent NADPH:protochlorophyllide oxidoreductase A O.I. C.G. H.G.
44.0 99.8 148.2 At1g67910 843119 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
42.5 99.8 43.6 At5g64110 836532 peroxidase, putative F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:membrane;PFOB O.I. C.G. H.G.
40.6 99.8 46.4 At4g35720 829724 unknown protein F:unknown;P:unknown;C:unknown;PO O.I. C.G. H.G.
39.7 99.8 39.1 At5g67060 836841 HEC1 (HECATE 1) F:transcription factor activity;P:transmitting tissue development, carpel formation, regulation of transcription;C:nucleus;PMBOFA O.I. C.G. H.G.
39.6 99.8 221.0 At1g06570 837168 PDS1 (PHYTOENE DESATURATION 1) Mutation of the PDS1 locus disrupts the activity of p-hydroxyphenylpyruvate dioxygenase (HPPDase), the first committed step in the synthesis of both plastoquinone and tocopherols in plants. O.I. C.G. H.G.
39.2 99.8 48.1 At5g44260 834449 zinc finger (CCCH-type) family protein F:transcription factor activity, nucleic acid binding;P:unknown;C:unknown;MOPFV O.I. C.G. H.G.
39.0 99.8 181.7 At5g01210 831901 transferase family protein F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFB O.I. C.G. H.G.
38.9 99.8 160.3 At1g64660 842774 ATMGL (ARABIDOPSIS THALIANA METHIONINE GAMMA-LYASE) Encodes a functional methionine gamma-lyase, a cytosolic enzyme catalyzes the degradation of methionine into methanethiol, alpha-ketobutyrate and ammonia. The catabolism of excess methionine is important to methionine homeostasis. O.I. C.G. H.G.
37.2 99.7 95.7 At3g05900 819759 neurofilament protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAV O.I. C.G. H.G.
36.3 99.7 160.9 At5g22500 832311 FAR1 (FATTY ACID REDUCTASE 1) F:oxidoreductase activity, acting on the CH-CH group of donors, fatty acyl-CoA reductase (alcohol-forming) activity;P:microsporogenesis, metabolic process;C:chloroplast;MBFOP O.I. C.G. H.G.
35.6 99.7 425.6 At3g47340 823888 ASN1 (GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1) encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell. O.I. C.G. H.G.
34.9 99.7 14.7 At3g01450 821140 binding F:binding;P:biological_process unknown;C:cellular_component unknown;MPOF O.I. C.G. H.G.
34.7 99.7 205.9 At1g09570 837483 PHYA (PHYTOCHROME A) Light-labile cytoplasmic red/far-red light photoreceptor involved in the regulation of photomorphogenesis. It exists in two inter-convertible forms: Pr and Pfr (active) and functions as a dimer.The N terminus carries a single tetrapyrrole chromophore, and the C terminus is involved in dimerization. It is the sole photoreceptor mediating the FR high irradiance response (HIR). Major regulator in red-light induction of phototropic enhancement. Involved in the regulation of de-etiolation. Involved in gravitropism and phototropism. Requires FHY1 for nuclear accumulation. O.I. C.G. H.G.
33.0 99.7 72.6 At5g62280 836349 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
32.9 99.7 275.0 At1g19530 838540 unknown protein F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;P O.I. C.G. H.G.
32.5 99.7 456.1 At2g37130 818289 peroxidase 21 (PER21) (P21) (PRXR5) F:electron carrier activity, peroxidase activity, heme binding;P:defense response to fungus;C:endomembrane system;PFO O.I. C.G. H.G.
32.4 99.7 167.8 At4g37220 829876 stress-responsive protein, putative F:molecular_function unknown;P:response to fructose stimulus, response to sucrose stimulus, response to glucose stimulus, response to stress;C:cellular_component unknown;P O.I. C.G. H.G.
32.2 99.7 207.0 At3g60140 825184 DIN2 (DARK INDUCIBLE 2) Encodes a protein similar to beta-glucosidase and is a member of glycoside hydrolase family 1. Expression is induced after 24 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell. O.I. C.G. H.G.
31.2 99.7 64.1 At5g63650 836485 SNRK2.5 (SNF1-RELATED PROTEIN KINASE 2.5) encodes a member of SNF1-related protein kinases (SnRK2) whose activity is activated by ionic (salt) and non-ionic (mannitol) osmotic stress. O.I. C.G. H.G.
30.2 99.7 286.4 At1g28330 839729 DYL1 (DORMANCY-ASSOCIATED PROTEIN-LIKE 1) dormancy-associated protein (DRM1) O.I. C.G. H.G.
29.4 99.7 41.6 At4g11610 826766 C2 domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOF O.I. C.G. H.G.
28.1 99.7 118.2 At1g15040 838069 glutamine amidotransferase-related F:hydrolase activity;P:glutamine metabolic process;C:cellular_component unknown;BOPAFM O.I. C.G. H.G.
27.5 99.7 32.8 At4g16670 827369 phosphoinositide binding F:phosphoinositide binding;P:signal transduction;C:cellular_component unknown;PFO O.I. C.G. H.G.
27.3 99.7 170.2 At2g18280 816344 AtTLP2 (TUBBY LIKE PROTEIN 2) Member of TLP family O.I. C.G. H.G.
27.1 99.7 192.7 At5g66170 836749 - F:molecular_function unknown;P:aging;C:cellular_component unknown;PBOA O.I. C.G. H.G.
26.5 99.7 75.2 At3g60530 825224 zinc finger (GATA type) family protein F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;PFOM O.I. C.G. H.G.
26.5 99.7 16.9 At1g21360 838735 GLTP2 (glycolipid transfer protein 2) F:glycolipid transporter activity, glycolipid binding;P:glycolipid transport;C:cytoplasm;P O.I. C.G. H.G.
26.0 99.7 17.9 At2g19660 816485 DC1 domain-containing protein F:molecular_function unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMO O.I. C.G. H.G.
25.9 99.7 67.1 At1g02340 839300 HFR1 (LONG HYPOCOTYL IN FAR-RED) Encodes a light-inducible, nuclear bHLH protein involved in phytochrome signaling. Mutants exhibit a long-hypocotyl phenotype only under far-red light but not under red light and are defective in other phytochrome A-related responses. Mutants also show blue light response defects. HFR1 interacts with COP1, co-localizes to the nuclear specks and is ubiquinated by COP1. O.I. C.G. H.G.
23.5 99.6 95.2 At3g48970 824058 copper-binding family protein F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:unknown;PBO O.I. C.G. H.G.
23.5 99.6 65.9 At5g02540 831913 short-chain dehydrogenase/reductase (SDR) family protein F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:unknown;BOMFPA O.I. C.G. H.G.
23.4 99.6 210.1 At5g03240 831899 UBQ3 (POLYUBIQUITIN 3) encodes ubiquitin that is attached to proteins destined for degradation. UBQ3 is most homologous with UBQ4, and is expressed in higher levels in vegetative tissue but lower levels in flowers than UBQ4. UBQ3 encodes different number of ubiquitins in different ecotypes. UBQ3 transcript level is modulated by UV-B and light/dark treatments. O.I. C.G. H.G.
23.4 99.6 50.3 At3g23880 821971 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:nucleus;PO O.I. C.G. H.G.
23.2 99.6 77.0 At1g21400 838739 2-oxoisovalerate dehydrogenase, putative / 3-methyl-2-oxobutanoate dehydrogenase, putative / branched-chain alpha-keto acid dehydrogenase E1 alpha subunit, putative F:oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity;P:metabolic process;C:unknown;BOMFPA O.I. C.G. H.G.
23.0 99.6 145.8 At3g06850 819869 BCE2 dihydrolipoamide branched chain acyltransferase O.I. C.G. H.G.
22.3 99.6 68.4 At3g50660 824229 DWF4 (DWARF 4) Encodes a 22α hydroxylase whose reaction is a rate-limiting step in brassinosteroid biosynthetic pathway. The protein is a member of CYP90B gene family. CLM is an epi-allele with small, compressed rosette, reduced internode length, and reduced fertility, appears in selfed ddm mutant plants possibly due to loss of cytosine methylation. Transcripts accumulate in actively growing tissues, and GUS expression is negatively regulated by brassinosteroids. Localized in the endoplasmic reticulum. The in vitro expressed protein can perform the C-22 hydroxylation of a variety of C27-, C28- and C29-sterols. Cholesterol was the best substrate, followed by campesterol. Sitosterol was a poor substrate. O.I. C.G. H.G.
22.3 99.6 28.0 At1g72070 843538 DNAJ heat shock N-terminal domain-containing protein F:unfolded protein binding, heat shock protein binding;P:protein folding;C:unknown;BOMPFAV O.I. C.G. H.G.
22.1 99.6 421.2 At5g49360 834996 BXL1 (BETA-XYLOSIDASE 1) Encodes a bifunctional {beta}-D-xylosidase/{alpha}-L-arabinofuranosidase required for pectic arabinan modification. Located in the extracellular matrix. Gene is expressed specifically in tissues undergoing secondary wall thickening. This is a member of glycosyl hydrolase family 3 and has six other closely related members. O.I. C.G. H.G.
21.4 99.6 170.9 At3g10740 820243 ASD1 (ALPHA-L-ARABINOFURANOSIDASE 1) Encodes a bifunctional alpha-l-arabinofuranosidase/beta-d-xylosidase that belongs to family 51 of glycoside hydrolases. It may be involved in cell wall modification. O.I. C.G. H.G.
21.2 99.6 322.5 At5g56870 835789 BGAL4 (beta-galactosidase 4) F:beta-galactosidase activity;P:lactose catabolic process, using glucoside 3-dehydrogenase, carbohydrate metabolic process, lactose catabolic process via UDP-galactose, lactose catabolic process;C:endomembrane system, beta-galactosidase complex;PBMFOA O.I. C.G. H.G.
20.8 99.6 258.1 At2g32150 817774 haloacid dehalogenase-like hydrolase family protein F:hydrolase activity, catalytic activity;P:metabolic process;C:cellular_component unknown;OBPFAM O.I. C.G. H.G.
20.8 99.6 33.1 At1g34760 840380 GRF11 (GENERAL REGULATORY FACTOR 11) Encodes a 14-3-3 protein. Binds H+-ATPase in response to blue light. O.I. C.G. H.G.
20.7 99.6 387.6 At2g05540 815103 glycine-rich protein F:unknown;P:unknown;C:endomembrane system;MPBOFVA O.I. C.G. H.G.
20.5 99.6 22.8 At1g55240 841967 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MP O.I. C.G. H.G.
20.3 99.6 159.8 At5g54080 835494 HGO (HOMOGENTISATE 1,2-DIOXYGENASE) homogentisate 1,2-dioxygenase O.I. C.G. H.G.
20.2 99.6 181.4 At3g61060 825278 AtPP2-A13 (Arabidopsis thaliana phloem protein 2-A13) F:carbohydrate binding;P:N-terminal protein myristoylation, response to wounding;C:unknown;P O.I. C.G. H.G.
20.1 99.6 46.4 At2g46740 819287 FAD-binding domain-containing protein F:oxidoreductase activity, D-arabinono-1,4-lactone oxidase activity, FAD binding, catalytic activity;P:unknown;C:cell wall;BOFPMA O.I. C.G. H.G.
20.0 99.6 83.8 At2g39980 818586 transferase family protein F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFB O.I. C.G. H.G.
19.3 99.6 34.7 At1g09530 837479 PIF3 (PHYTOCHROME INTERACTING FACTOR 3) Transcription factor interacting with photoreceptors phyA and phyB. Forms a ternary complex in vitro with G-box element of the promoters of LHY, CCA1. Acts as a negative regulator of phyB signalling. It degrades rapidly after irradiation of dark grown seedlings in a process controlled by phytochromes. Does not play a significant role in controlling light input and function of the circadian clockwork. Binds to G- and E-boxes, but not to other ACEs. Binds to anthocyanin biosynthetic genes in a light- and HY5-independent fashion. PIF3 function as a transcriptional activator can be functionally and mechanistically separated from its role in repression of PhyB mediated processes. O.I. C.G. H.G.
19.0 99.5 47.8 At4g16780 827384 ATHB-2 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 2) Encodes a homeodomain-leucine zipper protein that is rapidly and strongly induced by changes in the ratio of red to far-red light. It is also involved in cell expansion and cell proliferation and in the response to auxin. O.I. C.G. H.G.
18.8 99.5 18.5 At5g51670 835241 unknown protein F:unknown;P:biological_process unknown;C:chloroplast;POB O.I. C.G. H.G.
18.6 99.5 596.7 At1g62380 842536 ACO2 (ACC OXIDASE 2) Encodes a protein similar to 1-aminocyclopropane-1-carboxylic oxidase (ACC oxidase). Expression of the AtACO2 transcripts is affected by ethylene. O.I. C.G. H.G.
18.6 99.5 45.5 At2g43060 818908 transcription factor F:transcription factor activity;P:regulation of transcription;C:nucleus;P O.I. C.G. H.G.
18.6 99.5 17.5 At1g20390 3766766 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
18.2 99.5 212.2 At4g30140 829137 GDSL-motif lipase/hydrolase family protein F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBOFM O.I. C.G. H.G.
18.2 99.5 45.7 At1g79700 844309 ovule development protein, putative F:transcription factor activity, DNA binding;P:organ morphogenesis, regulation of transcription, DNA-dependent;C:nucleus;POB O.I. C.G. H.G.
17.6 99.5 166.5 At1g52190 841649 proton-dependent oligopeptide transport (POT) family protein F:transporter activity;P:oligopeptide transport;C:membrane;PBMFO O.I. C.G. H.G.
17.6 99.5 66.2 At5g04530 830332 KCS19 (3-KETOACYL-COA SYNTHASE 19) Encodes KCS19, a member of the 3-ketoacyl-CoA synthase family involved in the biosynthesis of VLCFA (very long chain fatty acids). O.I. C.G. H.G.
17.5 99.5 115.7 At1g58180 842185 carbonic anhydrase family protein / carbonate dehydratase family protein F:carbonate dehydratase activity, zinc ion binding;P:carbon utilization;C:mitochondrion;BOPFMA O.I. C.G. H.G.
17.5 99.5 111.9 At1g14890 838054 enzyme inhibitor/ pectinesterase/ pectinesterase inhibitor F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:unknown;P O.I. C.G. H.G.
17.5 99.5 24.5 At4g30410 829164 transcription factor F:transcription factor activity;P:unknown;C:unknown;PO O.I. C.G. H.G.
17.5 99.5 19.8 At5g66080 836740 protein phosphatase 2C family protein / PP2C family protein F:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:protein serine/threonine phosphatase complex;MPOFBV O.I. C.G. H.G.
17.3 99.5 178.1 At5g12250 831100 TUB6 (BETA-6 TUBULIN) Encodes a beta-tubulin. Expression of TUB6 has been shown to decrease in response to cold treatment. O.I. C.G. H.G.
17.3 99.5 146.9 At2g38400 818421 AGT3 (ALANINE:GLYOXYLATE AMINOTRANSFERASE 3) alanine:glyoxylate aminotransferase 2 homolog (AGT3) mRNA, O.I. C.G. H.G.
17.3 99.5 107.4 At2g37640 818341 EXP3 member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana. O.I. C.G. H.G.
17.2 99.5 121.9 At5g23660 832431 MTN3 (Arabidopsis homolog of Medicago truncatula MTN3) homolog of the Medicago nodulin MTN3 O.I. C.G. H.G.
17.0 99.5 106.4 At5g43580 834378 serine-type endopeptidase inhibitor Predicted to encode a PR (pathogenesis-related) peptide that belongs to the PR-6 proteinase inhibitor family. Six putative PR-6-type protein encoding genes are found in Arabidopsis: At2g38900, At2g38870, At5g43570, At5g43580, At3g50020 and At3g46860. O.I. C.G. H.G.
17.0 99.5 11.0 At2g46990 819313 IAA20 (INDOLE-3-ACETIC ACID INDUCIBLE 20) Encodes a member of the Aux/IAA family of proteins implicated in auxin signaling. IAA20 lacks the conserved degron (domain II) found in many family members, and IAA20 fusion proteins are stable in Arabidopsis seedlings. IAA20 transcripts are induced by auxin treatment, and overexpression of IAA20 leads to defects in gravitropism, root development, root meristem maintenance, etiolation, and cotyledon vascular development. O.I. C.G. H.G.
16.9 99.5 87.3 At1g26665 839207 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPO O.I. C.G. H.G.
16.9 99.5 59.6 At5g01740 831686 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PB O.I. C.G. H.G.
16.8 99.5 213.5 At3g26510 822258 octicosapeptide/Phox/Bem1p (PB1) domain-containing protein F:unknown;P:biological_process unknown;C:unknown;POFMBV O.I. C.G. H.G.
16.8 99.5 133.0 At4g33150 829452 lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme F:unknown;P:unknown;C:unknown;OBFMPA O.I. C.G. H.G.
16.5 99.5 33.6 At4g36380 829790 ROT3 (ROTUNDIFOLIA 3) Encodes a cytochrome P-450 gene that is involved in leaf blade expansion by controlling polar cell expansion in the leaf length direction. Member of the CYP90C CYP450 family. ROT3 was shown to be involved in brassinosteroid biosynthesis, most likely in the conversion step of typhasterol (TY) to castasterone (CS). As 6-deoxo-CS was unable to restore the phenotype of rot3-1, it has been postulated that ROT3 might be specifically involved in the conversion of TY to CS in the C6-oxidation pathway of brassinolide. Recently, CYP90C1 was shown to catalyse the C-23 hydroxylation of several brassinosteroids (the enzyme has a broad specificity for 22-hydroxylated substrates). O.I. C.G. H.G.
16.4 99.5 205.0 At5g47450 834794 AtTIP2 Tonoplast intrinsic protein, transports ammonium (NH3) and methylammonium across the tonoplast membrane, gene expression shows diurnal regulation and is upregulated by ammonium (NH3). O.I. C.G. H.G.
16.4 99.5 126.1 At4g34030 829549 MCCB (3-METHYLCROTONYL-COA CARBOXYLASE) MCC-B is involved in leucine degradation in mitochondria. The active protein is a dimer of MCC-A and MCC-B. MCC-A is biotinylated whereas MCC-B is not. O.I. C.G. H.G.
16.1 99.5 41.5 At4g08300 826384 nodulin MtN21 family protein F:unknown;P:unknown;C:membrane;BPOAMF O.I. C.G. H.G.
16.0 99.5 56.6 At1g23870 838998 ATTPS9 Encodes an enzyme putatively involved in trehalose biosynthesis. The protein has a trehalose synthase (TPS)-like domain that may or may not be active as well as a trehalose phosphatase (TPP)-like domain. O.I. C.G. H.G.
15.8 99.5 207.8 At2g20670 816595 unknown protein F:unknown;P:unknown;C:chloroplast;PO O.I. C.G. H.G.
15.8 99.5 132.8 At5g57655 835871 xylose isomerase family protein F:xylose isomerase activity;P:carbohydrate metabolic process;C:endoplasmic reticulum, plasma membrane, vacuole;BOPMF O.I. C.G. H.G.
15.6 99.5 32.1 At5g57760 835884 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
15.5 99.5 266.1 At5g09440 830803 EXL4 (EXORDIUM LIKE 4) F:molecular_function unknown;P:biological_process unknown;C:membrane;PB O.I. C.G. H.G.
15.5 99.5 89.1 At5g04470 830326 SIM (SIAMESE) Encodes a novel nuclear 14-kD protein containing a cyclin binding motif and a motif found in ICK/KRP cell cycle inhibitor proteins. It is required for coordinating cell division and cell differentiation during the development of Arabidopsis trichomes, playing a key role in the mitosis-to-endoreduplication transition. It interacts with D-type cyclins in vivo. O.I. C.G. H.G.
15.5 99.5 26.8 At2g42010 818802 PLDBETA1 (PHOSPHOLIPASE D BETA 1) phospholipase D (PLDbeta) O.I. C.G. H.G.
15.3 99.4 38.9 At4g36780 829831 transcription regulator F:transcription regulator activity;P:biological_process unknown;C:cellular_component unknown;PF O.I. C.G. H.G.
15.2 99.4 104.3 At4g38470 830003 protein kinase family protein F:protein serine/threonine/tyrosine kinase activity, protein kinase activity;P:protein amino acid phosphorylation, metabolic process;C:cytosol;MPOBFVA O.I. C.G. H.G.
15.0 99.4 86.6 At5g56100 835709 glycine-rich protein / oleosin F:molecular_function unknown;P:lipid storage;C:monolayer-surrounded lipid storage body, integral to membrane, membrane;PB O.I. C.G. H.G.

Std2 GX	%ile	Std GX	Gene ID	Repr. ID	Gene name	Functional description	O.I.	C.G.	H.G.
95.0	99.9	604.6	At4g14130	827051	XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7)	xyloglucan endotransglycosylase-related protein (XTR7)	O.I.	C.G.	H.G.
90.2	99.9	31.0	At1g27670	839659	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
84.2	99.9	71.8	At4g25580	828663	stress-responsive protein-related	F:unknown;P:unknown;C:cellular_component unknown;PMOFBV	O.I.	C.G.	H.G.
70.3	99.9	65.4	At5g57240	835830	ORP4C (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 4C)	F:oxysterol binding;P:steroid metabolic process;C:cellular_component unknown;MFOP	O.I.	C.G.	H.G.
69.1	99.9	66.1	At2g41850	818785	PGAZAT (POLYGALACTURONASE ABSCISSION ZONE A. THALIANA)	ADPG2.	O.I.	C.G.	H.G.
64.3	99.8	105.0	At3g30180	822709	BR6OX2 (BRASSINOSTEROID-6-OXIDASE 2)	Encodes a cytochrome p450 enzyme that catalyzes the last reaction in the production of brassinolide. It is capable of converting 6-deoxocastasterone into castasterone, a C-6 oxidation, as well as the further conversion of castasterone into brassinolide by a Baeyer-Villinger oxidation reaction at C-6, resulting in the formation of an unusual seven-membered lactone ring. The enzyme possesses high affinity for both C28- and C27-Brassinosteroids. The expression of the gene using a CYP85A2 promoter:LUC fusion construct was shown to be under circadian and light control.	O.I.	C.G.	H.G.
61.8	99.8	257.1	At1g10070	837543	ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2)	Encodes a chloroplast branched-chain amino acid aminotransferase. Complements the yeast leu/iso-leu/val auxotrophy mutant.	O.I.	C.G.	H.G.
54.8	99.8	98.1	At5g53980	835481	ATHB52 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 52)	Encodes a homeodomain leucine zipper class I (HD-Zip I) protein.	O.I.	C.G.	H.G.
54.7	99.8	239.0	At1g12080	837760	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA	O.I.	C.G.	H.G.
50.9	99.8	131.6	At5g44440	834471	FAD-binding domain-containing protein	F:electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity;P:unknown;C:endomembrane system;BFPOAM	O.I.	C.G.	H.G.
48.5	99.8	107.7	At1g62770	842576	invertase/pectin methylesterase inhibitor family protein	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
48.3	99.8	228.4	At1g03090	838362	MCCA	MCCA is the biotinylated subunit of the dimer MCCase, which is involved in leucine degradation. Both subunits are nuclear coded and the active enzyme is located in the mitochondrion.	O.I.	C.G.	H.G.
47.0	99.8	173.3	At3g45300	823668	IVD (ISOVALERYL-COA-DEHYDROGENASE)	Encodes isovaleryl-coenzyme a dehydrogenase.	O.I.	C.G.	H.G.
44.8	99.8	144.2	At5g54190	835507	PORA	light-dependent NADPH:protochlorophyllide oxidoreductase A	O.I.	C.G.	H.G.
44.0	99.8	148.2	At1g67910	843119	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
42.5	99.8	43.6	At5g64110	836532	peroxidase, putative	F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:membrane;PFOB	O.I.	C.G.	H.G.
40.6	99.8	46.4	At4g35720	829724	unknown protein	F:unknown;P:unknown;C:unknown;PO	O.I.	C.G.	H.G.
39.7	99.8	39.1	At5g67060	836841	HEC1 (HECATE 1)	F:transcription factor activity;P:transmitting tissue development, carpel formation, regulation of transcription;C:nucleus;PMBOFA	O.I.	C.G.	H.G.
39.6	99.8	221.0	At1g06570	837168	PDS1 (PHYTOENE DESATURATION 1)	Mutation of the PDS1 locus disrupts the activity of p-hydroxyphenylpyruvate dioxygenase (HPPDase), the first committed step in the synthesis of both plastoquinone and tocopherols in plants.	O.I.	C.G.	H.G.
39.2	99.8	48.1	At5g44260	834449	zinc finger (CCCH-type) family protein	F:transcription factor activity, nucleic acid binding;P:unknown;C:unknown;MOPFV	O.I.	C.G.	H.G.
39.0	99.8	181.7	At5g01210	831901	transferase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFB	O.I.	C.G.	H.G.
38.9	99.8	160.3	At1g64660	842774	ATMGL (ARABIDOPSIS THALIANA METHIONINE GAMMA-LYASE)	Encodes a functional methionine gamma-lyase, a cytosolic enzyme catalyzes the degradation of methionine into methanethiol, alpha-ketobutyrate and ammonia. The catabolism of excess methionine is important to methionine homeostasis.	O.I.	C.G.	H.G.
37.2	99.7	95.7	At3g05900	819759	neurofilament protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAV	O.I.	C.G.	H.G.
36.3	99.7	160.9	At5g22500	832311	FAR1 (FATTY ACID REDUCTASE 1)	F:oxidoreductase activity, acting on the CH-CH group of donors, fatty acyl-CoA reductase (alcohol-forming) activity;P:microsporogenesis, metabolic process;C:chloroplast;MBFOP	O.I.	C.G.	H.G.
35.6	99.7	425.6	At3g47340	823888	ASN1 (GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1)	encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell.	O.I.	C.G.	H.G.
34.9	99.7	14.7	At3g01450	821140	binding	F:binding;P:biological_process unknown;C:cellular_component unknown;MPOF	O.I.	C.G.	H.G.
34.7	99.7	205.9	At1g09570	837483	PHYA (PHYTOCHROME A)	Light-labile cytoplasmic red/far-red light photoreceptor involved in the regulation of photomorphogenesis. It exists in two inter-convertible forms: Pr and Pfr (active) and functions as a dimer.The N terminus carries a single tetrapyrrole chromophore, and the C terminus is involved in dimerization. It is the sole photoreceptor mediating the FR high irradiance response (HIR). Major regulator in red-light induction of phototropic enhancement. Involved in the regulation of de-etiolation. Involved in gravitropism and phototropism. Requires FHY1 for nuclear accumulation.	O.I.	C.G.	H.G.
33.0	99.7	72.6	At5g62280	836349	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
32.9	99.7	275.0	At1g19530	838540	unknown protein	F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;P	O.I.	C.G.	H.G.
32.5	99.7	456.1	At2g37130	818289	peroxidase 21 (PER21) (P21) (PRXR5)	F:electron carrier activity, peroxidase activity, heme binding;P:defense response to fungus;C:endomembrane system;PFO	O.I.	C.G.	H.G.
32.4	99.7	167.8	At4g37220	829876	stress-responsive protein, putative	F:molecular_function unknown;P:response to fructose stimulus, response to sucrose stimulus, response to glucose stimulus, response to stress;C:cellular_component unknown;P	O.I.	C.G.	H.G.
32.2	99.7	207.0	At3g60140	825184	DIN2 (DARK INDUCIBLE 2)	Encodes a protein similar to beta-glucosidase and is a member of glycoside hydrolase family 1. Expression is induced after 24 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell.	O.I.	C.G.	H.G.
31.2	99.7	64.1	At5g63650	836485	SNRK2.5 (SNF1-RELATED PROTEIN KINASE 2.5)	encodes a member of SNF1-related protein kinases (SnRK2) whose activity is activated by ionic (salt) and non-ionic (mannitol) osmotic stress.	O.I.	C.G.	H.G.
30.2	99.7	286.4	At1g28330	839729	DYL1 (DORMANCY-ASSOCIATED PROTEIN-LIKE 1)	dormancy-associated protein (DRM1)	O.I.	C.G.	H.G.
29.4	99.7	41.6	At4g11610	826766	C2 domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOF	O.I.	C.G.	H.G.
28.1	99.7	118.2	At1g15040	838069	glutamine amidotransferase-related	F:hydrolase activity;P:glutamine metabolic process;C:cellular_component unknown;BOPAFM	O.I.	C.G.	H.G.
27.5	99.7	32.8	At4g16670	827369	phosphoinositide binding	F:phosphoinositide binding;P:signal transduction;C:cellular_component unknown;PFO	O.I.	C.G.	H.G.
27.3	99.7	170.2	At2g18280	816344	AtTLP2 (TUBBY LIKE PROTEIN 2)	Member of TLP family	O.I.	C.G.	H.G.
27.1	99.7	192.7	At5g66170	836749	-	F:molecular_function unknown;P:aging;C:cellular_component unknown;PBOA	O.I.	C.G.	H.G.
26.5	99.7	75.2	At3g60530	825224	zinc finger (GATA type) family protein	F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;PFOM	O.I.	C.G.	H.G.
26.5	99.7	16.9	At1g21360	838735	GLTP2 (glycolipid transfer protein 2)	F:glycolipid transporter activity, glycolipid binding;P:glycolipid transport;C:cytoplasm;P	O.I.	C.G.	H.G.
26.0	99.7	17.9	At2g19660	816485	DC1 domain-containing protein	F:molecular_function unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMO	O.I.	C.G.	H.G.
25.9	99.7	67.1	At1g02340	839300	HFR1 (LONG HYPOCOTYL IN FAR-RED)	Encodes a light-inducible, nuclear bHLH protein involved in phytochrome signaling. Mutants exhibit a long-hypocotyl phenotype only under far-red light but not under red light and are defective in other phytochrome A-related responses. Mutants also show blue light response defects. HFR1 interacts with COP1, co-localizes to the nuclear specks and is ubiquinated by COP1.	O.I.	C.G.	H.G.
23.5	99.6	95.2	At3g48970	824058	copper-binding family protein	F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:unknown;PBO	O.I.	C.G.	H.G.
23.5	99.6	65.9	At5g02540	831913	short-chain dehydrogenase/reductase (SDR) family protein	F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:unknown;BOMFPA	O.I.	C.G.	H.G.
23.4	99.6	210.1	At5g03240	831899	UBQ3 (POLYUBIQUITIN 3)	encodes ubiquitin that is attached to proteins destined for degradation. UBQ3 is most homologous with UBQ4, and is expressed in higher levels in vegetative tissue but lower levels in flowers than UBQ4. UBQ3 encodes different number of ubiquitins in different ecotypes. UBQ3 transcript level is modulated by UV-B and light/dark treatments.	O.I.	C.G.	H.G.
23.4	99.6	50.3	At3g23880	821971	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:nucleus;PO	O.I.	C.G.	H.G.
23.2	99.6	77.0	At1g21400	838739	2-oxoisovalerate dehydrogenase, putative / 3-methyl-2-oxobutanoate dehydrogenase, putative / branched-chain alpha-keto acid dehydrogenase E1 alpha subunit, putative	F:oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity;P:metabolic process;C:unknown;BOMFPA	O.I.	C.G.	H.G.
23.0	99.6	145.8	At3g06850	819869	BCE2	dihydrolipoamide branched chain acyltransferase	O.I.	C.G.	H.G.
22.3	99.6	68.4	At3g50660	824229	DWF4 (DWARF 4)	Encodes a 22α hydroxylase whose reaction is a rate-limiting step in brassinosteroid biosynthetic pathway. The protein is a member of CYP90B gene family. CLM is an epi-allele with small, compressed rosette, reduced internode length, and reduced fertility, appears in selfed ddm mutant plants possibly due to loss of cytosine methylation. Transcripts accumulate in actively growing tissues, and GUS expression is negatively regulated by brassinosteroids. Localized in the endoplasmic reticulum. The in vitro expressed protein can perform the C-22 hydroxylation of a variety of C27-, C28- and C29-sterols. Cholesterol was the best substrate, followed by campesterol. Sitosterol was a poor substrate.	O.I.	C.G.	H.G.
22.3	99.6	28.0	At1g72070	843538	DNAJ heat shock N-terminal domain-containing protein	F:unfolded protein binding, heat shock protein binding;P:protein folding;C:unknown;BOMPFAV	O.I.	C.G.	H.G.
22.1	99.6	421.2	At5g49360	834996	BXL1 (BETA-XYLOSIDASE 1)	Encodes a bifunctional {beta}-D-xylosidase/{alpha}-L-arabinofuranosidase required for pectic arabinan modification. Located in the extracellular matrix. Gene is expressed specifically in tissues undergoing secondary wall thickening. This is a member of glycosyl hydrolase family 3 and has six other closely related members.	O.I.	C.G.	H.G.
21.4	99.6	170.9	At3g10740	820243	ASD1 (ALPHA-L-ARABINOFURANOSIDASE 1)	Encodes a bifunctional alpha-l-arabinofuranosidase/beta-d-xylosidase that belongs to family 51 of glycoside hydrolases. It may be involved in cell wall modification.	O.I.	C.G.	H.G.
21.2	99.6	322.5	At5g56870	835789	BGAL4 (beta-galactosidase 4)	F:beta-galactosidase activity;P:lactose catabolic process, using glucoside 3-dehydrogenase, carbohydrate metabolic process, lactose catabolic process via UDP-galactose, lactose catabolic process;C:endomembrane system, beta-galactosidase complex;PBMFOA	O.I.	C.G.	H.G.
20.8	99.6	258.1	At2g32150	817774	haloacid dehalogenase-like hydrolase family protein	F:hydrolase activity, catalytic activity;P:metabolic process;C:cellular_component unknown;OBPFAM	O.I.	C.G.	H.G.
20.8	99.6	33.1	At1g34760	840380	GRF11 (GENERAL REGULATORY FACTOR 11)	Encodes a 14-3-3 protein. Binds H+-ATPase in response to blue light.	O.I.	C.G.	H.G.
20.7	99.6	387.6	At2g05540	815103	glycine-rich protein	F:unknown;P:unknown;C:endomembrane system;MPBOFVA	O.I.	C.G.	H.G.
20.5	99.6	22.8	At1g55240	841967	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MP	O.I.	C.G.	H.G.
20.3	99.6	159.8	At5g54080	835494	HGO (HOMOGENTISATE 1,2-DIOXYGENASE)	homogentisate 1,2-dioxygenase	O.I.	C.G.	H.G.
20.2	99.6	181.4	At3g61060	825278	AtPP2-A13 (Arabidopsis thaliana phloem protein 2-A13)	F:carbohydrate binding;P:N-terminal protein myristoylation, response to wounding;C:unknown;P	O.I.	C.G.	H.G.
20.1	99.6	46.4	At2g46740	819287	FAD-binding domain-containing protein	F:oxidoreductase activity, D-arabinono-1,4-lactone oxidase activity, FAD binding, catalytic activity;P:unknown;C:cell wall;BOFPMA	O.I.	C.G.	H.G.
20.0	99.6	83.8	At2g39980	818586	transferase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFB	O.I.	C.G.	H.G.
19.3	99.6	34.7	At1g09530	837479	PIF3 (PHYTOCHROME INTERACTING FACTOR 3)	Transcription factor interacting with photoreceptors phyA and phyB. Forms a ternary complex in vitro with G-box element of the promoters of LHY, CCA1. Acts as a negative regulator of phyB signalling. It degrades rapidly after irradiation of dark grown seedlings in a process controlled by phytochromes. Does not play a significant role in controlling light input and function of the circadian clockwork. Binds to G- and E-boxes, but not to other ACEs. Binds to anthocyanin biosynthetic genes in a light- and HY5-independent fashion. PIF3 function as a transcriptional activator can be functionally and mechanistically separated from its role in repression of PhyB mediated processes.	O.I.	C.G.	H.G.
19.0	99.5	47.8	At4g16780	827384	ATHB-2 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 2)	Encodes a homeodomain-leucine zipper protein that is rapidly and strongly induced by changes in the ratio of red to far-red light. It is also involved in cell expansion and cell proliferation and in the response to auxin.	O.I.	C.G.	H.G.
18.8	99.5	18.5	At5g51670	835241	unknown protein	F:unknown;P:biological_process unknown;C:chloroplast;POB	O.I.	C.G.	H.G.
18.6	99.5	596.7	At1g62380	842536	ACO2 (ACC OXIDASE 2)	Encodes a protein similar to 1-aminocyclopropane-1-carboxylic oxidase (ACC oxidase). Expression of the AtACO2 transcripts is affected by ethylene.	O.I.	C.G.	H.G.
18.6	99.5	45.5	At2g43060	818908	transcription factor	F:transcription factor activity;P:regulation of transcription;C:nucleus;P	O.I.	C.G.	H.G.
18.6	99.5	17.5	At1g20390	3766766	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
18.2	99.5	212.2	At4g30140	829137	GDSL-motif lipase/hydrolase family protein	F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBOFM	O.I.	C.G.	H.G.
18.2	99.5	45.7	At1g79700	844309	ovule development protein, putative	F:transcription factor activity, DNA binding;P:organ morphogenesis, regulation of transcription, DNA-dependent;C:nucleus;POB	O.I.	C.G.	H.G.
17.6	99.5	166.5	At1g52190	841649	proton-dependent oligopeptide transport (POT) family protein	F:transporter activity;P:oligopeptide transport;C:membrane;PBMFO	O.I.	C.G.	H.G.
17.6	99.5	66.2	At5g04530	830332	KCS19 (3-KETOACYL-COA SYNTHASE 19)	Encodes KCS19, a member of the 3-ketoacyl-CoA synthase family involved in the biosynthesis of VLCFA (very long chain fatty acids).	O.I.	C.G.	H.G.
17.5	99.5	115.7	At1g58180	842185	carbonic anhydrase family protein / carbonate dehydratase family protein	F:carbonate dehydratase activity, zinc ion binding;P:carbon utilization;C:mitochondrion;BOPFMA	O.I.	C.G.	H.G.
17.5	99.5	111.9	At1g14890	838054	enzyme inhibitor/ pectinesterase/ pectinesterase inhibitor	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:unknown;P	O.I.	C.G.	H.G.
17.5	99.5	24.5	At4g30410	829164	transcription factor	F:transcription factor activity;P:unknown;C:unknown;PO	O.I.	C.G.	H.G.
17.5	99.5	19.8	At5g66080	836740	protein phosphatase 2C family protein / PP2C family protein	F:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:protein serine/threonine phosphatase complex;MPOFBV	O.I.	C.G.	H.G.
17.3	99.5	178.1	At5g12250	831100	TUB6 (BETA-6 TUBULIN)	Encodes a beta-tubulin. Expression of TUB6 has been shown to decrease in response to cold treatment.	O.I.	C.G.	H.G.
17.3	99.5	146.9	At2g38400	818421	AGT3 (ALANINE:GLYOXYLATE AMINOTRANSFERASE 3)	alanine:glyoxylate aminotransferase 2 homolog (AGT3) mRNA,	O.I.	C.G.	H.G.
17.3	99.5	107.4	At2g37640	818341	EXP3	member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana.	O.I.	C.G.	H.G.
17.2	99.5	121.9	At5g23660	832431	MTN3 (Arabidopsis homolog of Medicago truncatula MTN3)	homolog of the Medicago nodulin MTN3	O.I.	C.G.	H.G.
17.0	99.5	106.4	At5g43580	834378	serine-type endopeptidase inhibitor	Predicted to encode a PR (pathogenesis-related) peptide that belongs to the PR-6 proteinase inhibitor family. Six putative PR-6-type protein encoding genes are found in Arabidopsis: At2g38900, At2g38870, At5g43570, At5g43580, At3g50020 and At3g46860.	O.I.	C.G.	H.G.
17.0	99.5	11.0	At2g46990	819313	IAA20 (INDOLE-3-ACETIC ACID INDUCIBLE 20)	Encodes a member of the Aux/IAA family of proteins implicated in auxin signaling. IAA20 lacks the conserved degron (domain II) found in many family members, and IAA20 fusion proteins are stable in Arabidopsis seedlings. IAA20 transcripts are induced by auxin treatment, and overexpression of IAA20 leads to defects in gravitropism, root development, root meristem maintenance, etiolation, and cotyledon vascular development.	O.I.	C.G.	H.G.
16.9	99.5	87.3	At1g26665	839207	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPO	O.I.	C.G.	H.G.
16.9	99.5	59.6	At5g01740	831686	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PB	O.I.	C.G.	H.G.
16.8	99.5	213.5	At3g26510	822258	octicosapeptide/Phox/Bem1p (PB1) domain-containing protein	F:unknown;P:biological_process unknown;C:unknown;POFMBV	O.I.	C.G.	H.G.
16.8	99.5	133.0	At4g33150	829452	lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme	F:unknown;P:unknown;C:unknown;OBFMPA	O.I.	C.G.	H.G.
16.5	99.5	33.6	At4g36380	829790	ROT3 (ROTUNDIFOLIA 3)	Encodes a cytochrome P-450 gene that is involved in leaf blade expansion by controlling polar cell expansion in the leaf length direction. Member of the CYP90C CYP450 family. ROT3 was shown to be involved in brassinosteroid biosynthesis, most likely in the conversion step of typhasterol (TY) to castasterone (CS). As 6-deoxo-CS was unable to restore the phenotype of rot3-1, it has been postulated that ROT3 might be specifically involved in the conversion of TY to CS in the C6-oxidation pathway of brassinolide. Recently, CYP90C1 was shown to catalyse the C-23 hydroxylation of several brassinosteroids (the enzyme has a broad specificity for 22-hydroxylated substrates).	O.I.	C.G.	H.G.
16.4	99.5	205.0	At5g47450	834794	AtTIP2	Tonoplast intrinsic protein, transports ammonium (NH3) and methylammonium across the tonoplast membrane, gene expression shows diurnal regulation and is upregulated by ammonium (NH3).	O.I.	C.G.	H.G.
16.4	99.5	126.1	At4g34030	829549	MCCB (3-METHYLCROTONYL-COA CARBOXYLASE)	MCC-B is involved in leucine degradation in mitochondria. The active protein is a dimer of MCC-A and MCC-B. MCC-A is biotinylated whereas MCC-B is not.	O.I.	C.G.	H.G.
16.1	99.5	41.5	At4g08300	826384	nodulin MtN21 family protein	F:unknown;P:unknown;C:membrane;BPOAMF	O.I.	C.G.	H.G.
16.0	99.5	56.6	At1g23870	838998	ATTPS9	Encodes an enzyme putatively involved in trehalose biosynthesis. The protein has a trehalose synthase (TPS)-like domain that may or may not be active as well as a trehalose phosphatase (TPP)-like domain.	O.I.	C.G.	H.G.
15.8	99.5	207.8	At2g20670	816595	unknown protein	F:unknown;P:unknown;C:chloroplast;PO	O.I.	C.G.	H.G.
15.8	99.5	132.8	At5g57655	835871	xylose isomerase family protein	F:xylose isomerase activity;P:carbohydrate metabolic process;C:endoplasmic reticulum, plasma membrane, vacuole;BOPMF	O.I.	C.G.	H.G.
15.6	99.5	32.1	At5g57760	835884	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
15.5	99.5	266.1	At5g09440	830803	EXL4 (EXORDIUM LIKE 4)	F:molecular_function unknown;P:biological_process unknown;C:membrane;PB	O.I.	C.G.	H.G.
15.5	99.5	89.1	At5g04470	830326	SIM (SIAMESE)	Encodes a novel nuclear 14-kD protein containing a cyclin binding motif and a motif found in ICK/KRP cell cycle inhibitor proteins. It is required for coordinating cell division and cell differentiation during the development of Arabidopsis trichomes, playing a key role in the mitosis-to-endoreduplication transition. It interacts with D-type cyclins in vivo.	O.I.	C.G.	H.G.
15.5	99.5	26.8	At2g42010	818802	PLDBETA1 (PHOSPHOLIPASE D BETA 1)	phospholipase D (PLDbeta)	O.I.	C.G.	H.G.
15.3	99.4	38.9	At4g36780	829831	transcription regulator	F:transcription regulator activity;P:biological_process unknown;C:cellular_component unknown;PF	O.I.	C.G.	H.G.
15.2	99.4	104.3	At4g38470	830003	protein kinase family protein	F:protein serine/threonine/tyrosine kinase activity, protein kinase activity;P:protein amino acid phosphorylation, metabolic process;C:cytosol;MPOBFVA	O.I.	C.G.	H.G.
15.0	99.4	86.6	At5g56100	835709	glycine-rich protein / oleosin	F:molecular_function unknown;P:lipid storage;C:monolayer-surrounded lipid storage body, integral to membrane, membrane;PB	O.I.	C.G.	H.G.

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GSM ID	GSM282698
Assay name	Col_BRZ_rep2
GSE experiment	GSE11216: Brassinazole treatment of arf2 and wild-type dark-grown seedlings

Microarray experiments to specifically-expressed genes

GSM ID GSM282698 Assay name Col_BRZ_rep2 GSE experiment GSE11216: Brassinazole treatment of arf2 and wild-type dark-grown seedlings

GSM ID GSM282698

Assay name Col_BRZ_rep2

GSE experiment GSE11216: Brassinazole treatment of arf2 and wild-type dark-grown seedlings