CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM109109

Assay name wild-type(Col-0) 1 day, biological rep3

GSE experiment GSE4847: Expression data from tocopherol deficient seedlings of Arabidopsis

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
288.9 100.0 404.6 At1g29090 839784 peptidase C1A papain family protein F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis;C:endomembrane system;MOPVBAF O.I. C.G. H.G.
108.2 99.9 64.6 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.
92.3 99.9 443.7 At4g36880 829841 CP1 (CYSTEINE PROTEINASE1) F:cysteine-type peptidase activity, cysteine-type endopeptidase activity;P:proteolysis, response to gibberellin stimulus, response to red light;C:endomembrane system;MOPVBAF O.I. C.G. H.G.
87.0 99.9 55.3 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.
67.1 99.8 291.2 At1g02640 837940 BXL2 (BETA-XYLOSIDASE 2) encodes a protein similar to a beta-xylosidase located in the extracellular matrix. This is a member of glycosyl hydrolase family 3 and has six other closely related members. O.I. C.G. H.G.
61.7 99.8 288.7 At1g73120 843643 unknown protein F:molecular_function unknown;P:response to oxidative stress;C:unknown;P O.I. C.G. H.G.
56.8 99.8 33.4 At2g43140 818916 DNA binding / transcription factor F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PMOBF O.I. C.G. H.G.
52.1 99.8 663.0 At3g21720 821726 ICL (ISOCITRATE LYASE) Encodes a glyoxylate cycle enzyme isocitrate lyase (ICL). O.I. C.G. H.G.
50.4 99.8 394.2 At5g03860 831690 MLS (MALATE SYNTHASE) Encodes a protein with malate synthase activity. O.I. C.G. H.G.
47.0 99.8 258.4 At3g45310 823669 cysteine proteinase, putative F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis;C:endomembrane system;MOPBVAF O.I. C.G. H.G.
43.4 99.8 419.5 At4g14690 827119 ELIP2 (EARLY LIGHT-INDUCIBLE PROTEIN 2) Encodes an early light-induced protein. ELIPs are thought not to be directly involved in the synthesis and assembly of specific photosynthetic complexes, but rather affect the biogenesis of all chlorophyll-binding complexes. A study (PMID 17553115) has shown that the chlorophyll synthesis pathway was downregulated as a result of constitutive ELIP2 expression, leading to decreased chlorophyll availability for the assembly of pigment-binding proteins for photosynthesis. O.I. C.G. H.G.
39.2 99.8 252.7 At2g22780 816808 PMDH1 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 1) encodes an peroxisomal NAD-malate dehydrogenase that is involved in fatty acid beta-oxidation through providing NAD to the process of converting fatty acyl CoA to acetyl CoA. O.I. C.G. H.G.
35.4 99.7 61.6 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.
35.0 99.7 266.6 At2g30970 817648 ASP1 (ASPARTATE AMINOTRANSFERASE 1) ASPARTATE AMINOTRANSFERASE 1 O.I. C.G. H.G.
32.5 99.7 163.2 At1g55020 841944 LOX1 lipoxygenase, a defense gene conferring resistance Xanthomonas campestris O.I. C.G. H.G.
28.3 99.7 24.1 At2g03590 814888 ATUPS1 (ARABIDOPSIS THALIANA UREIDE PERMEASE 1) Encodes a member of a class of allantoin transporters. O.I. C.G. H.G.
27.3 99.7 270.1 At5g42890 834300 SCP2 (STEROL CARRIER PROTEIN 2) F:sterol carrier activity, oxidoreductase activity;P:glyoxylate metabolic process, intracellular lipid transport, fatty acid beta-oxidation, seed germination;C:peroxisome;MFOPB O.I. C.G. H.G.
27.0 99.7 165.2 At4g01700 828131 chitinase, putative F:chitinase activity;P:cell wall macromolecule catabolic process;C:cell wall;PBOMVF O.I. C.G. H.G.
25.3 99.6 11.7 At1g65340 842842 CYP96A3 member of CYP96A O.I. C.G. H.G.
22.7 99.6 228.4 At3g06860 819870 MFP2 (MULTIFUNCTIONAL PROTEIN 2) Encodes a multifunctional protein. Involved in peroxisomal fatty acid beta oxidation. Loss-of-function mutant lacks hydroxyacyl-CoA dehydrogenase activity and have reduced levels of long-chain enoyl-CoA hydratase activity. The mutant has fewer but larger peroxisomes. O.I. C.G. H.G.
22.2 99.6 52.2 At4g21490 828234 NDB3 F:NADH dehydrogenase activity;P:unknown;C:unknown;BOFPAM O.I. C.G. H.G.
22.0 99.6 37.4 At1g29080 839783 peptidase C1A papain family protein F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis;C:endomembrane system;MOPVBAF O.I. C.G. H.G.
21.9 99.6 171.7 At5g14450 831296 GDSL-motif lipase/hydrolase family protein F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:plant-type cell wall;PBFOM O.I. C.G. H.G.
20.8 99.6 131.0 At2g47780 819390 rubber elongation factor (REF) protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
20.5 99.6 34.3 At3g23790 821961 AMP-binding protein, putative F:catalytic activity;P:metabolic process;C:chloroplast envelope;BOMFPAV O.I. C.G. H.G.
20.0 99.6 40.9 At1g60090 842304 BGLU4 (BETA GLUCOSIDASE 4) F:cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:endomembrane system;BOPMFA O.I. C.G. H.G.
19.3 99.6 60.6 At5g63810 836501 BGAL10 (beta-galactosidase 10) member of Glycoside Hydrolase Family 35 O.I. C.G. H.G.
18.6 99.5 69.2 At1g33790 840271 jacalin lectin family protein F:unknown;P:biological_process unknown;C:chloroplast;PO O.I. C.G. H.G.
18.5 99.5 98.4 At3g48460 824005 GDSL-motif lipase/hydrolase family protein F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:glycerol biosynthetic process, lipid metabolic process;C:endomembrane system;PBOFM O.I. C.G. H.G.
18.3 99.5 40.4 At5g58900 836007 myb family transcription factor F:transcription factor activity, DNA binding;P:regulation of transcription;C:unknown;PMOF O.I. C.G. H.G.
17.6 99.5 292.8 At5g11520 831024 ASP3 (ASPARTATE AMINOTRANSFERASE 3) Encodes the chloroplastic isozyme of aspartate aminotransferase. Involved in aspartate biosynthesis and nitrogen metabolism. mRNA is expressed in senescing leaves. O.I. C.G. H.G.
17.2 99.5 276.6 At3g22840 821855 ELIP1 (EARLY LIGHT-INDUCABLE PROTEIN) Encodes an early light-inducible protein. O.I. C.G. H.G.
17.0 99.5 238.3 At1g54000 841838 myrosinase-associated protein, putative F:lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:vacuolar membrane, plasma membrane, vacuole, plant-type cell wall, plant-type vacuole;PBOFM O.I. C.G. H.G.
17.0 99.5 198.1 At3g44990 823634 XTR8 (XYLOGLUCAN ENDO-TRANSGLYCOSYLASE-RELATED 8) xyloglucan endo-transglycosylase O.I. C.G. H.G.
16.8 99.5 64.6 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.
16.6 99.5 21.5 At2g32560 817817 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO O.I. C.G. H.G.
16.6 99.5 10.4 At2g14060 815891 S-adenosyl-L-methionine:carboxyl methyltransferase family protein encodes a protein whose sequence is similar to SAM:salicylic acid carboxyl methyltransferase (SAMT) (GI:6002712)(Clarkia breweri) and to SAM:benzoic acid carboxyl methyltransferase (BAMT)(GI:9789277)(Antirrhinum majus) O.I. C.G. H.G.
16.0 99.5 147.0 At3g61070 825279 PEX11E member of the peroxin11 (PEX11) gene family, integral to peroxisome membrane, controls peroxisome proliferation. O.I. C.G. H.G.
16.0 99.5 141.0 At2g02040 814735 PTR2 (PEPTIDE TRANSPORTER 2) Encodes a di- and tri-peptide transporter that recognizes a variety of different amino acid combinations. Expression of the transcripts for this gene can be detected in the embryo through in situ hybridization. This protein does not have nitrate transporter activity based on oocyte transport assays. O.I. C.G. H.G.
15.6 99.5 70.8 At1g43780 840974 scpl44 (serine carboxypeptidase-like 44) F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFBO O.I. C.G. H.G.
15.2 99.4 398.5 At4g37870 829943 PCK1 (PHOSPHOENOLPYRUVATE CARBOXYKINASE 1) Encodes a putative phosphoenolpyruvate carboxykinase (ATP-dependent). O.I. C.G. H.G.
15.2 99.4 74.8 At5g02260 831736 ATEXPA9 (ARABIDOPSIS THALIANA EXPANSIN A9) member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio) O.I. C.G. H.G.
14.5 99.4 30.2 At2g41850 818785 PGAZAT (POLYGALACTURONASE ABSCISSION ZONE A. THALIANA) ADPG2. O.I. C.G. H.G.
14.4 99.4 21.9 At5g27410 832800 aminotransferase class IV family protein F:catalytic activity;P:metabolic process;C:cellular_component unknown;OBPAFM O.I. C.G. H.G.
14.3 99.4 129.9 At4g12910 826903 scpl20 (serine carboxypeptidase-like 20) F:serine-type carboxypeptidase activity;P:proteolysis;C:vacuole;PMFOB O.I. C.G. H.G.
14.1 99.4 32.9 At1g55760 842025 BTB/POZ domain-containing protein F:protein binding;P:biological_process unknown;C:unknown;MPOVF O.I. C.G. H.G.
13.5 99.4 104.7 At5g56260 835725 dimethylmenaquinone methyltransferase family protein F:ribonuclease inhibitor activity;P:regulation of RNA metabolic process;C:cellular_component unknown;BOPAFM O.I. C.G. H.G.
13.4 99.4 142.4 At5g05290 830411 ATEXPA2 (ARABIDOPSIS THALIANA EXPANSIN A2) Encodes an expansin. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio) O.I. C.G. H.G.
13.4 99.4 42.6 At1g29120 839787 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;FPMO O.I. C.G. H.G.
13.1 99.4 386.4 At2g05710 815120 aconitate hydratase, cytoplasmic, putative / citrate hydro-lyase/aconitase, putative Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds. O.I. C.G. H.G.
12.9 99.3 16.0 At4g37580 829913 HLS1 (HOOKLESS 1) involved in apical hook development. putative N-acetyltransferase O.I. C.G. H.G.
12.8 99.3 12.1 At4g25990 828705 CIL chloroplast import apparatus CIA2-like. CIA2 is a transcription factor which upregulates chloroplast translocon genes O.I. C.G. H.G.
12.5 99.3 60.5 At5g45650 834605 subtilase family protein F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:endomembrane system;BPOFAM O.I. C.G. H.G.
12.3 99.3 14.4 At1g80340 844374 GA3OX2 (GIBBERELLIN 3-OXIDASE 2) Encodes a protein with gibberellin 3 β-hydroxylase activity. The protein was heterologously expressed in E. coli and shown to catalyze the hydroxylation of both GA9 and GA20. O.I. C.G. H.G.
12.2 99.3 118.1 At1g54030 841841 GDSL-motif lipase, putative F:lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:vacuole;PBOFM O.I. C.G. H.G.
12.0 99.3 25.7 At2g34020 817963 calcium ion binding F:calcium ion binding;P:biological_process unknown;C:unknown;POMBF O.I. C.G. H.G.
11.8 99.3 102.2 At3g14220 820640 GDSL-motif lipase/hydrolase family protein F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:vacuole;PBOFM O.I. C.G. H.G.
11.6 99.3 242.5 At5g43060 834321 cysteine proteinase, putative / thiol protease, putative F:cysteine-type peptidase activity, cysteine-type endopeptidase activity;P:response to salt stress;C:vacuole;MOPVBAF O.I. C.G. H.G.
11.6 99.3 182.2 At5g20950 832220 glycosyl hydrolase family 3 protein F:hydrolase activity, hydrolyzing O-glycosyl compounds;P:carbohydrate metabolic process;C:cell wall, membrane, plant-type cell wall;BOFPAM O.I. C.G. H.G.
11.5 99.3 124.1 At5g65110 836635 ACX2 (ACYL-COA OXIDASE 2) Encodes an acyl-CoA oxidase presumably involved in long chain fatty acid biosynthesis. O.I. C.G. H.G.
11.4 99.3 91.3 At5g66920 836826 sks17 (SKU5 Similar 17) F:oxidoreductase activity, copper ion binding;P:unknown;C:cell wall, plant-type cell wall;FBPMOA O.I. C.G. H.G.
11.1 99.2 173.8 At4g32460 829381 - F:molecular_function unknown;P:biological_process unknown;C:plant-type cell wall;PB O.I. C.G. H.G.
10.9 99.2 148.3 At1g06290 837140 ACX3 (ACYL-COA OXIDASE 3) Encodes an acyl-CoA oxidase with specificity for medium chain fatty acids. O.I. C.G. H.G.
10.7 99.2 127.8 At2g42790 818879 CSY3 (citrate synthase 3) Encodes a peroxisomal citrate synthase that is expressed throughout seedling and shoot development. O.I. C.G. H.G.
10.5 99.2 74.3 At4g16210 827314 ECHIA (ENOYL-COA HYDRATASE/ISOMERASE A) F:catalytic activity;P:metabolic process;C:peroxisome;BOMFPA O.I. C.G. H.G.
10.4 99.2 26.9 At4g19230 827663 CYP707A1 Encodes a protein with ABA 8'-hydroxylase activity, involved in ABA catabolism. Member of the CYP707A gene family. CYP707A1 appears to play an important role in determining the ABA levels in dry seeds. Gene involved in postgermination growth. Overexpression of CYP707A1 leads to a decrease in ABA levels and a reduction in after-ripening period to break dormancy. O.I. C.G. H.G.
10.2 99.2 50.3 At3g47800 823934 aldose 1-epimerase family protein F:aldose 1-epimerase activity;P:galactose metabolic process, hexose metabolic process, carbohydrate metabolic process;C:endomembrane system;BOMFPA O.I. C.G. H.G.
10.1 99.2 63.4 At1g67810 843107 SUFE2 (SULFUR E 2) Encodes a protein capable of stimulating the cysteine desulfurase activity of CpNifS (AT1G08490) in vitro. SufE2:GFP localizes to the chloroplasts where it is likely to play a role in iron-sulfur cluster assembly. Transcript levels for this gene are high in the pollen relative to other organs based on RT-PCR analysis. O.I. C.G. H.G.
9.8 99.1 21.7 At4g09740 826560 AtGH9B14 (Arabidopsis thaliana glycosyl hydrolase 9B14) F:hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:endomembrane system;PBMOF O.I. C.G. H.G.
9.5 99.1 58.8 At5g23310 832395 FSD3 (FE SUPEROXIDE DISMUTASE 3) Fe superoxide dismutase O.I. C.G. H.G.
9.4 99.1 55.3 At2g24280 816963 serine carboxypeptidase S28 family protein F:serine-type peptidase activity, serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system, lysosome;MOFPB O.I. C.G. H.G.
9.3 99.1 37.2 At5g39080 833900 transferase family protein F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFO O.I. C.G. H.G.
9.1 99.1 25.7 At2g46950 819309 CYP709B2 member of CYP709B O.I. C.G. H.G.
8.8 99.0 112.3 At5g08260 830722 scpl35 (serine carboxypeptidase-like 35) F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFOB O.I. C.G. H.G.
8.7 99.0 19.2 At5g05880 830473 UDP-glucoronosyl/UDP-glucosyl transferase family protein F:UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBVOF O.I. C.G. H.G.
8.6 99.0 7.6 At1g65590 842871 HEXO3 (BETA-HEXOSAMINIDASE 3) Encodes a protein with beta-hexosaminidase activity. Located on the plasma membrane. 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.
288.9	100.0	404.6	At1g29090	839784	peptidase C1A papain family protein	F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis;C:endomembrane system;MOPVBAF	O.I.	C.G.	H.G.
108.2	99.9	64.6	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.
92.3	99.9	443.7	At4g36880	829841	CP1 (CYSTEINE PROTEINASE1)	F:cysteine-type peptidase activity, cysteine-type endopeptidase activity;P:proteolysis, response to gibberellin stimulus, response to red light;C:endomembrane system;MOPVBAF	O.I.	C.G.	H.G.
87.0	99.9	55.3	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.
67.1	99.8	291.2	At1g02640	837940	BXL2 (BETA-XYLOSIDASE 2)	encodes a protein similar to a beta-xylosidase located in the extracellular matrix. This is a member of glycosyl hydrolase family 3 and has six other closely related members.	O.I.	C.G.	H.G.
61.7	99.8	288.7	At1g73120	843643	unknown protein	F:molecular_function unknown;P:response to oxidative stress;C:unknown;P	O.I.	C.G.	H.G.
56.8	99.8	33.4	At2g43140	818916	DNA binding / transcription factor	F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PMOBF	O.I.	C.G.	H.G.
52.1	99.8	663.0	At3g21720	821726	ICL (ISOCITRATE LYASE)	Encodes a glyoxylate cycle enzyme isocitrate lyase (ICL).	O.I.	C.G.	H.G.
50.4	99.8	394.2	At5g03860	831690	MLS (MALATE SYNTHASE)	Encodes a protein with malate synthase activity.	O.I.	C.G.	H.G.
47.0	99.8	258.4	At3g45310	823669	cysteine proteinase, putative	F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis;C:endomembrane system;MOPBVAF	O.I.	C.G.	H.G.
43.4	99.8	419.5	At4g14690	827119	ELIP2 (EARLY LIGHT-INDUCIBLE PROTEIN 2)	Encodes an early light-induced protein. ELIPs are thought not to be directly involved in the synthesis and assembly of specific photosynthetic complexes, but rather affect the biogenesis of all chlorophyll-binding complexes. A study (PMID 17553115) has shown that the chlorophyll synthesis pathway was downregulated as a result of constitutive ELIP2 expression, leading to decreased chlorophyll availability for the assembly of pigment-binding proteins for photosynthesis.	O.I.	C.G.	H.G.
39.2	99.8	252.7	At2g22780	816808	PMDH1 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 1)	encodes an peroxisomal NAD-malate dehydrogenase that is involved in fatty acid beta-oxidation through providing NAD to the process of converting fatty acyl CoA to acetyl CoA.	O.I.	C.G.	H.G.
35.4	99.7	61.6	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.
35.0	99.7	266.6	At2g30970	817648	ASP1 (ASPARTATE AMINOTRANSFERASE 1)	ASPARTATE AMINOTRANSFERASE 1	O.I.	C.G.	H.G.
32.5	99.7	163.2	At1g55020	841944	LOX1	lipoxygenase, a defense gene conferring resistance Xanthomonas campestris	O.I.	C.G.	H.G.
28.3	99.7	24.1	At2g03590	814888	ATUPS1 (ARABIDOPSIS THALIANA UREIDE PERMEASE 1)	Encodes a member of a class of allantoin transporters.	O.I.	C.G.	H.G.
27.3	99.7	270.1	At5g42890	834300	SCP2 (STEROL CARRIER PROTEIN 2)	F:sterol carrier activity, oxidoreductase activity;P:glyoxylate metabolic process, intracellular lipid transport, fatty acid beta-oxidation, seed germination;C:peroxisome;MFOPB	O.I.	C.G.	H.G.
27.0	99.7	165.2	At4g01700	828131	chitinase, putative	F:chitinase activity;P:cell wall macromolecule catabolic process;C:cell wall;PBOMVF	O.I.	C.G.	H.G.
25.3	99.6	11.7	At1g65340	842842	CYP96A3	member of CYP96A	O.I.	C.G.	H.G.
22.7	99.6	228.4	At3g06860	819870	MFP2 (MULTIFUNCTIONAL PROTEIN 2)	Encodes a multifunctional protein. Involved in peroxisomal fatty acid beta oxidation. Loss-of-function mutant lacks hydroxyacyl-CoA dehydrogenase activity and have reduced levels of long-chain enoyl-CoA hydratase activity. The mutant has fewer but larger peroxisomes.	O.I.	C.G.	H.G.
22.2	99.6	52.2	At4g21490	828234	NDB3	F:NADH dehydrogenase activity;P:unknown;C:unknown;BOFPAM	O.I.	C.G.	H.G.
22.0	99.6	37.4	At1g29080	839783	peptidase C1A papain family protein	F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis;C:endomembrane system;MOPVBAF	O.I.	C.G.	H.G.
21.9	99.6	171.7	At5g14450	831296	GDSL-motif lipase/hydrolase family protein	F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:plant-type cell wall;PBFOM	O.I.	C.G.	H.G.
20.8	99.6	131.0	At2g47780	819390	rubber elongation factor (REF) protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
20.5	99.6	34.3	At3g23790	821961	AMP-binding protein, putative	F:catalytic activity;P:metabolic process;C:chloroplast envelope;BOMFPAV	O.I.	C.G.	H.G.
20.0	99.6	40.9	At1g60090	842304	BGLU4 (BETA GLUCOSIDASE 4)	F:cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:endomembrane system;BOPMFA	O.I.	C.G.	H.G.
19.3	99.6	60.6	At5g63810	836501	BGAL10 (beta-galactosidase 10)	member of Glycoside Hydrolase Family 35	O.I.	C.G.	H.G.
18.6	99.5	69.2	At1g33790	840271	jacalin lectin family protein	F:unknown;P:biological_process unknown;C:chloroplast;PO	O.I.	C.G.	H.G.
18.5	99.5	98.4	At3g48460	824005	GDSL-motif lipase/hydrolase family protein	F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:glycerol biosynthetic process, lipid metabolic process;C:endomembrane system;PBOFM	O.I.	C.G.	H.G.
18.3	99.5	40.4	At5g58900	836007	myb family transcription factor	F:transcription factor activity, DNA binding;P:regulation of transcription;C:unknown;PMOF	O.I.	C.G.	H.G.
17.6	99.5	292.8	At5g11520	831024	ASP3 (ASPARTATE AMINOTRANSFERASE 3)	Encodes the chloroplastic isozyme of aspartate aminotransferase. Involved in aspartate biosynthesis and nitrogen metabolism. mRNA is expressed in senescing leaves.	O.I.	C.G.	H.G.
17.2	99.5	276.6	At3g22840	821855	ELIP1 (EARLY LIGHT-INDUCABLE PROTEIN)	Encodes an early light-inducible protein.	O.I.	C.G.	H.G.
17.0	99.5	238.3	At1g54000	841838	myrosinase-associated protein, putative	F:lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:vacuolar membrane, plasma membrane, vacuole, plant-type cell wall, plant-type vacuole;PBOFM	O.I.	C.G.	H.G.
17.0	99.5	198.1	At3g44990	823634	XTR8 (XYLOGLUCAN ENDO-TRANSGLYCOSYLASE-RELATED 8)	xyloglucan endo-transglycosylase	O.I.	C.G.	H.G.
16.8	99.5	64.6	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.
16.6	99.5	21.5	At2g32560	817817	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO	O.I.	C.G.	H.G.
16.6	99.5	10.4	At2g14060	815891	S-adenosyl-L-methionine:carboxyl methyltransferase family protein	encodes a protein whose sequence is similar to SAM:salicylic acid carboxyl methyltransferase (SAMT) (GI:6002712)(Clarkia breweri) and to SAM:benzoic acid carboxyl methyltransferase (BAMT)(GI:9789277)(Antirrhinum majus)	O.I.	C.G.	H.G.
16.0	99.5	147.0	At3g61070	825279	PEX11E	member of the peroxin11 (PEX11) gene family, integral to peroxisome membrane, controls peroxisome proliferation.	O.I.	C.G.	H.G.
16.0	99.5	141.0	At2g02040	814735	PTR2 (PEPTIDE TRANSPORTER 2)	Encodes a di- and tri-peptide transporter that recognizes a variety of different amino acid combinations. Expression of the transcripts for this gene can be detected in the embryo through in situ hybridization. This protein does not have nitrate transporter activity based on oocyte transport assays.	O.I.	C.G.	H.G.
15.6	99.5	70.8	At1g43780	840974	scpl44 (serine carboxypeptidase-like 44)	F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFBO	O.I.	C.G.	H.G.
15.2	99.4	398.5	At4g37870	829943	PCK1 (PHOSPHOENOLPYRUVATE CARBOXYKINASE 1)	Encodes a putative phosphoenolpyruvate carboxykinase (ATP-dependent).	O.I.	C.G.	H.G.
15.2	99.4	74.8	At5g02260	831736	ATEXPA9 (ARABIDOPSIS THALIANA EXPANSIN A9)	member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio)	O.I.	C.G.	H.G.
14.5	99.4	30.2	At2g41850	818785	PGAZAT (POLYGALACTURONASE ABSCISSION ZONE A. THALIANA)	ADPG2.	O.I.	C.G.	H.G.
14.4	99.4	21.9	At5g27410	832800	aminotransferase class IV family protein	F:catalytic activity;P:metabolic process;C:cellular_component unknown;OBPAFM	O.I.	C.G.	H.G.
14.3	99.4	129.9	At4g12910	826903	scpl20 (serine carboxypeptidase-like 20)	F:serine-type carboxypeptidase activity;P:proteolysis;C:vacuole;PMFOB	O.I.	C.G.	H.G.
14.1	99.4	32.9	At1g55760	842025	BTB/POZ domain-containing protein	F:protein binding;P:biological_process unknown;C:unknown;MPOVF	O.I.	C.G.	H.G.
13.5	99.4	104.7	At5g56260	835725	dimethylmenaquinone methyltransferase family protein	F:ribonuclease inhibitor activity;P:regulation of RNA metabolic process;C:cellular_component unknown;BOPAFM	O.I.	C.G.	H.G.
13.4	99.4	142.4	At5g05290	830411	ATEXPA2 (ARABIDOPSIS THALIANA EXPANSIN A2)	Encodes an expansin. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio)	O.I.	C.G.	H.G.
13.4	99.4	42.6	At1g29120	839787	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;FPMO	O.I.	C.G.	H.G.
13.1	99.4	386.4	At2g05710	815120	aconitate hydratase, cytoplasmic, putative / citrate hydro-lyase/aconitase, putative	Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.	O.I.	C.G.	H.G.
12.9	99.3	16.0	At4g37580	829913	HLS1 (HOOKLESS 1)	involved in apical hook development. putative N-acetyltransferase	O.I.	C.G.	H.G.
12.8	99.3	12.1	At4g25990	828705	CIL	chloroplast import apparatus CIA2-like. CIA2 is a transcription factor which upregulates chloroplast translocon genes	O.I.	C.G.	H.G.
12.5	99.3	60.5	At5g45650	834605	subtilase family protein	F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:endomembrane system;BPOFAM	O.I.	C.G.	H.G.
12.3	99.3	14.4	At1g80340	844374	GA3OX2 (GIBBERELLIN 3-OXIDASE 2)	Encodes a protein with gibberellin 3 β-hydroxylase activity. The protein was heterologously expressed in E. coli and shown to catalyze the hydroxylation of both GA9 and GA20.	O.I.	C.G.	H.G.
12.2	99.3	118.1	At1g54030	841841	GDSL-motif lipase, putative	F:lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:vacuole;PBOFM	O.I.	C.G.	H.G.
12.0	99.3	25.7	At2g34020	817963	calcium ion binding	F:calcium ion binding;P:biological_process unknown;C:unknown;POMBF	O.I.	C.G.	H.G.
11.8	99.3	102.2	At3g14220	820640	GDSL-motif lipase/hydrolase family protein	F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:vacuole;PBOFM	O.I.	C.G.	H.G.
11.6	99.3	242.5	At5g43060	834321	cysteine proteinase, putative / thiol protease, putative	F:cysteine-type peptidase activity, cysteine-type endopeptidase activity;P:response to salt stress;C:vacuole;MOPVBAF	O.I.	C.G.	H.G.
11.6	99.3	182.2	At5g20950	832220	glycosyl hydrolase family 3 protein	F:hydrolase activity, hydrolyzing O-glycosyl compounds;P:carbohydrate metabolic process;C:cell wall, membrane, plant-type cell wall;BOFPAM	O.I.	C.G.	H.G.
11.5	99.3	124.1	At5g65110	836635	ACX2 (ACYL-COA OXIDASE 2)	Encodes an acyl-CoA oxidase presumably involved in long chain fatty acid biosynthesis.	O.I.	C.G.	H.G.
11.4	99.3	91.3	At5g66920	836826	sks17 (SKU5 Similar 17)	F:oxidoreductase activity, copper ion binding;P:unknown;C:cell wall, plant-type cell wall;FBPMOA	O.I.	C.G.	H.G.
11.1	99.2	173.8	At4g32460	829381	-	F:molecular_function unknown;P:biological_process unknown;C:plant-type cell wall;PB	O.I.	C.G.	H.G.
10.9	99.2	148.3	At1g06290	837140	ACX3 (ACYL-COA OXIDASE 3)	Encodes an acyl-CoA oxidase with specificity for medium chain fatty acids.	O.I.	C.G.	H.G.
10.7	99.2	127.8	At2g42790	818879	CSY3 (citrate synthase 3)	Encodes a peroxisomal citrate synthase that is expressed throughout seedling and shoot development.	O.I.	C.G.	H.G.
10.5	99.2	74.3	At4g16210	827314	ECHIA (ENOYL-COA HYDRATASE/ISOMERASE A)	F:catalytic activity;P:metabolic process;C:peroxisome;BOMFPA	O.I.	C.G.	H.G.
10.4	99.2	26.9	At4g19230	827663	CYP707A1	Encodes a protein with ABA 8'-hydroxylase activity, involved in ABA catabolism. Member of the CYP707A gene family. CYP707A1 appears to play an important role in determining the ABA levels in dry seeds. Gene involved in postgermination growth. Overexpression of CYP707A1 leads to a decrease in ABA levels and a reduction in after-ripening period to break dormancy.	O.I.	C.G.	H.G.
10.2	99.2	50.3	At3g47800	823934	aldose 1-epimerase family protein	F:aldose 1-epimerase activity;P:galactose metabolic process, hexose metabolic process, carbohydrate metabolic process;C:endomembrane system;BOMFPA	O.I.	C.G.	H.G.
10.1	99.2	63.4	At1g67810	843107	SUFE2 (SULFUR E 2)	Encodes a protein capable of stimulating the cysteine desulfurase activity of CpNifS (AT1G08490) in vitro. SufE2:GFP localizes to the chloroplasts where it is likely to play a role in iron-sulfur cluster assembly. Transcript levels for this gene are high in the pollen relative to other organs based on RT-PCR analysis.	O.I.	C.G.	H.G.
9.8	99.1	21.7	At4g09740	826560	AtGH9B14 (Arabidopsis thaliana glycosyl hydrolase 9B14)	F:hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:endomembrane system;PBMOF	O.I.	C.G.	H.G.
9.5	99.1	58.8	At5g23310	832395	FSD3 (FE SUPEROXIDE DISMUTASE 3)	Fe superoxide dismutase	O.I.	C.G.	H.G.
9.4	99.1	55.3	At2g24280	816963	serine carboxypeptidase S28 family protein	F:serine-type peptidase activity, serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system, lysosome;MOFPB	O.I.	C.G.	H.G.
9.3	99.1	37.2	At5g39080	833900	transferase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFO	O.I.	C.G.	H.G.
9.1	99.1	25.7	At2g46950	819309	CYP709B2	member of CYP709B	O.I.	C.G.	H.G.
8.8	99.0	112.3	At5g08260	830722	scpl35 (serine carboxypeptidase-like 35)	F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFOB	O.I.	C.G.	H.G.
8.7	99.0	19.2	At5g05880	830473	UDP-glucoronosyl/UDP-glucosyl transferase family protein	F:UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBVOF	O.I.	C.G.	H.G.
8.6	99.0	7.6	At1g65590	842871	HEXO3 (BETA-HEXOSAMINIDASE 3)	Encodes a protein with beta-hexosaminidase activity. Located on the plasma membrane.	O.I.	C.G.	H.G.

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GSM ID	GSM109109
Assay name	wild-type(Col-0) 1 day, biological rep3
GSE experiment	GSE4847: Expression data from tocopherol deficient seedlings of Arabidopsis

Microarray experiments to specifically-expressed genes

GSM ID GSM109109 Assay name wild-type(Col-0) 1 day, biological rep3 GSE experiment GSE4847: Expression data from tocopherol deficient seedlings of Arabidopsis

GSM ID GSM109109

Assay name wild-type(Col-0) 1 day, biological rep3

GSE experiment GSE4847: Expression data from tocopherol deficient seedlings of Arabidopsis