CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM134366

Assay name St.Clair_1-27_449_Cvi-1_0.02%-silwet_Rep3_ATH1

GSE experiment GSE5753: Expression Level Polymorphism Project (ELP) - Cvi-1

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
56.1 99.8 59.2 At1g78450 844181 SOUL heme-binding family protein F:binding;P:biological_process unknown;C:endomembrane system;OMPBA O.I. C.G. H.G.
51.9 99.8 61.8 At1g58025 842169 DNA binding F:DNA binding;P:biological_process unknown;C:cellular_component unknown;MOFBPV O.I. C.G. H.G.
45.5 99.8 28.2 At1g31680 - - O.I. C.G. H.G.
39.1 99.8 76.6 At1g31690 840056 amine oxidase/ copper ion binding / quinone binding F:quinone binding, amine oxidase activity, copper ion binding;P:cellular amine metabolic process;C:endomembrane system;FBMOPA O.I. C.G. H.G.
29.3 99.7 199.2 At4g03060 828102 AOP2 (ALKENYL HYDROXALKYL PRODUCING 2) Encodes a truncated and null function protein, due to a 5-bp deletion in cDNA. The functional allele in ecotype Cvi, AOP2, encodes a 2-oxoglutarate-dependent dioxygenase which is involved in glucosinolate biosynthesis. The natural variation in this locus explains the diversification of alkenyl glucosinolate among different ecotypes of Arabidopsis. O.I. C.G. H.G.
24.5 99.6 76.7 At5g10140 830878 FLC (FLOWERING LOCUS C) MADS-box protein encoded by FLOWERING LOCUS C - transcription factor that functions as a repressor of floral transition and contributes to temperature compensation of the circadian clock. Expression is downregulated during cold treatment. Vernalization, FRI and the autonomous pathway all influence the state of FLC chromatin. Both maternal and paternal alleles are reset by vernalization, but their earliest activation differs in timing and location. Histone H3 trimethylation at lysine 4 and histone acetylation are associated with active FLC expression, whereas histone deacetylation and histone H3 dimethylation at lysines 9 and 27 are involved in FLC repression. Expression is also repressed by two small RNAs (30- and 24-nt) complementary to the FLC sense strand 3� to the polyA site. The small RNAs are most likely derived from an antisense transcript of FLC. Interacts with SOC1 and FT chromatin in vivo. Member of a protein complex. O.I. C.G. H.G.
23.8 99.6 56.0 At1g14230 837984 nucleoside phosphatase family protein / GDA1/CD39 family protein F:hydrolase activity;P:unknown;C:unknown;MFPOB O.I. C.G. H.G.
21.5 99.6 22.1 At3g19350 821469 MPC (MATERNALLY EXPRESSED PAB C-TERMINAL) Encodes a the C-terminal domain of poly(A) binding proteins. MPC is imprinted such that only the maternal allele is expressed in the endosperm. MPC is silenced by the action of MET1 and its expression is promoted by DEM. O.I. C.G. H.G.
19.6 99.6 26.6 At1g28610 839761 GDSL-motif lipase, putative F:lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBM O.I. C.G. H.G.
19.5 99.6 19.4 At1g52770 841710 phototropic-responsive NPH3 family protein F:signal transducer activity;P:response to light stimulus;C:cellular_component unknown;P O.I. C.G. H.G.
19.2 99.6 10.1 At2g22920 816823 serine carboxypeptidase S10 family protein F:serine-type carboxypeptidase activity;P:proteolysis;C:plant-type cell wall;PMFBO O.I. C.G. H.G.
19.0 99.5 123.9 At2g40750 818670 WRKY54 member of WRKY Transcription Factor; Group III O.I. C.G. H.G.
18.1 99.5 13.1 At4g29610 829082 cytidine deaminase, putative / cytidine aminohydrolase, putative F:hydrolase activity, cytidine deaminase activity, zinc ion binding, catalytic activity;P:cytidine deamination, cytidine metabolic process;C:cellular_component unknown;BOMPFA O.I. C.G. H.G.
17.8 99.5 80.1 At1g13470 837907 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. C.G. H.G.
17.7 99.5 13.3 At2g47570 819370 60S ribosomal protein L18 (RPL18A) F:structural constituent of ribosome;P:translation;C:cytosolic large ribosomal subunit, large ribosomal subunit;MOFPA O.I. C.G. H.G.
15.8 99.5 74.6 At5g42900 834301 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
15.6 99.5 17.2 At1g59620 842252 CW9 Encodes CW9. O.I. C.G. H.G.
15.3 99.4 12.7 At5g24480 832519 beta-galactosidase F:beta-galactosidase activity;P:carbohydrate metabolic process;C:beta-galactosidase complex;P O.I. C.G. H.G.
15.0 99.4 37.6 At3g07650 819956 COL9 (CONSTANS-LIKE 9) This gene belongs to the CO (CONSTANS) gene family. This gene family is divided in three subgroups: groups III, to which COL9 belongs, is characterised by one B-box (supposed to regulate protein-protein interactions) and a second diverged zinc finger. COL9 downregulates expression of CO (CONSTANS) as well as FT and SOC1 which are known regulatory targets of CO. O.I. C.G. H.G.
13.4 99.4 25.0 At3g04650 819623 oxidoreductase F:oxidoreductase activity;P:unknown;C:chloroplast;OBPAMF O.I. C.G. H.G.
13.0 99.4 14.7 At5g61290 836250 flavin-containing monooxygenase family protein / FMO family protein F:NADP or NADPH binding, monooxygenase activity, FAD binding, flavin-containing monooxygenase activity;P:unknown;C:cellular_component unknown;BOMFPA O.I. C.G. H.G.
12.8 99.3 45.2 At4g37150 829869 MES9 (METHYL ESTERASE 9) Encodes a protein shown to have carboxylesterase activity, methyl salicylate esterase activity, methyl jasmonate esterase activity, and methyl IAA esterase activity in vitro. MES9 appears to be involved in MeSA hydrolysis in planta. Expression of MES9 can restore systemic acquired resistance in SAR-deficient tobacco plants. This protein does not act on MeGA4, or MEGA9 in vitro. O.I. C.G. H.G.
12.7 99.3 76.1 At5g10180 830882 AST68 Encodes a low-affinity sulfate transporter expressed in the root cap and central cylinder, where it is induced by sulfur starvation. Expression in the shoot vascular system is not induced by sulfur starvation. O.I. C.G. H.G.
12.2 99.3 6.3 At5g18880 832006 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
11.7 99.3 73.2 At2g22980 816829 serine-type carboxypeptidase F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFBO O.I. C.G. H.G.
10.6 99.2 36.6 At5g50450 835113 zinc finger (MYND type) family protein F:binding, zinc ion binding;P:biological_process unknown;C:cellular_component unknown;FPBMO O.I. C.G. H.G.
10.5 99.2 29.5 At5g38290 833811 peptidyl-tRNA hydrolase family protein F:aminoacyl-tRNA hydrolase activity;P:translation;C:chloroplast;BOPFM O.I. C.G. H.G.
10.4 99.2 19.9 At3g21950 821753 methyltransferase F:methyltransferase activity;P:response to cadmium ion;C:cellular_component unknown;POBMF O.I. C.G. H.G.
10.3 99.2 135.9 At1g70890 843427 MLP43 (MLP-LIKE PROTEIN 43) F:molecular_function unknown;P:response to biotic stimulus, defense response;C:chloroplast;P O.I. C.G. H.G.
10.2 99.2 69.0 At5g52540 835330 unknown protein F:unknown;P:unknown;C:chloroplast envelope;BOPA O.I. C.G. H.G.
10.2 99.2 34.0 At1g07050 837216 CONSTANS-like protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POF O.I. C.G. H.G.
10.1 99.2 5.0 At5g28560 832953 unknown protein F:molecular_function unknown;P:biological_process unknown;C:vacuole O.I. C.G. H.G.
9.8 99.1 160.9 At1g21250 838721 WAK1 (CELL WALL-ASSOCIATED KINASE) cell wall-associated kinase, may function as a signaling receptor of extracellular matrix component. O.I. C.G. H.G.
9.7 99.1 133.6 At5g54960 835587 PDC2 (pyruvate decarboxylase-2) pyruvate decarboxylase-2 O.I. C.G. H.G.
9.7 99.1 9.4 At3g25020 822093 AtRLP42 (Receptor Like Protein 42) F:protein binding;P:signal transduction, defense response;C:endomembrane system;PMOBFAV O.I. C.G. H.G.
9.5 99.1 24.0 At5g48250 834878 zinc finger (B-box type) family protein F:transcription factor activity, zinc ion binding;P:unknown;C:plasma membrane;POM O.I. C.G. H.G.
9.4 99.1 9.1 At1g17665 838343 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;OPMF O.I. C.G. H.G.
9.3 99.1 48.0 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.
9.1 99.1 23.2 At5g60100 836132 APRR3 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 3) Encodes pseudo-response regulator 3 (APRR3/PRR3). PRR3 transcript levels vary in a circadian pattern with peak expression at dusk under long and short day conditions. PRR3 affects the period of the circadian clock and seedlings with reduced levels of PRR3 have shorter periods, based on transcriptional assays of clock-regulated genes. PRR3 is expressed in the vasculature of cotyledons and leaves where it may help stabilize the TOC1 protein by preventing interactions between TOC1 and the F-box protein ZTL. O.I. C.G. H.G.
9.0 99.1 8.7 At2g30420 817593 ETC2 In a tandem repeat with AT2G30424 and AT2G30432 O.I. C.G. H.G.
8.8 99.0 102.3 At5g63780 836498 SHA1 (shoot apical meristem arrest 1) Encodes SHA1 (shoot apical meristem arrest), a putative E3 ligase (a RING finger protein) required for post-embryonic SAM maintenance. The mutant sha1-1 shows a primary SAM-deficient phenotype at the adult stage. O.I. C.G. H.G.
8.8 99.0 21.5 At2g24120 816946 SCA3 (SCABRA 3) F:DNA-directed RNA polymerase activity, DNA binding;P:transcription;C:mitochondrion;OFPMVB O.I. C.G. H.G.
8.7 99.0 33.0 At3g03090 821117 AtVGT1 (Arabidopsis thaliana vacuolar glucose transporter 1) Encodes a vacuolar membrane-localized glucose transporter that can also transport fructose. Mutations in these gene have effects on seed germination and time to flowering. 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.
56.1	99.8	59.2	At1g78450	844181	SOUL heme-binding family protein	F:binding;P:biological_process unknown;C:endomembrane system;OMPBA	O.I.	C.G.	H.G.
51.9	99.8	61.8	At1g58025	842169	DNA binding	F:DNA binding;P:biological_process unknown;C:cellular_component unknown;MOFBPV	O.I.	C.G.	H.G.
45.5	99.8	28.2	At1g31680		-	-	O.I.	C.G.	H.G.
39.1	99.8	76.6	At1g31690	840056	amine oxidase/ copper ion binding / quinone binding	F:quinone binding, amine oxidase activity, copper ion binding;P:cellular amine metabolic process;C:endomembrane system;FBMOPA	O.I.	C.G.	H.G.
29.3	99.7	199.2	At4g03060	828102	AOP2 (ALKENYL HYDROXALKYL PRODUCING 2)	Encodes a truncated and null function protein, due to a 5-bp deletion in cDNA. The functional allele in ecotype Cvi, AOP2, encodes a 2-oxoglutarate-dependent dioxygenase which is involved in glucosinolate biosynthesis. The natural variation in this locus explains the diversification of alkenyl glucosinolate among different ecotypes of Arabidopsis.	O.I.	C.G.	H.G.
24.5	99.6	76.7	At5g10140	830878	FLC (FLOWERING LOCUS C)	MADS-box protein encoded by FLOWERING LOCUS C - transcription factor that functions as a repressor of floral transition and contributes to temperature compensation of the circadian clock. Expression is downregulated during cold treatment. Vernalization, FRI and the autonomous pathway all influence the state of FLC chromatin. Both maternal and paternal alleles are reset by vernalization, but their earliest activation differs in timing and location. Histone H3 trimethylation at lysine 4 and histone acetylation are associated with active FLC expression, whereas histone deacetylation and histone H3 dimethylation at lysines 9 and 27 are involved in FLC repression. Expression is also repressed by two small RNAs (30- and 24-nt) complementary to the FLC sense strand 3� to the polyA site. The small RNAs are most likely derived from an antisense transcript of FLC. Interacts with SOC1 and FT chromatin in vivo. Member of a protein complex.	O.I.	C.G.	H.G.
23.8	99.6	56.0	At1g14230	837984	nucleoside phosphatase family protein / GDA1/CD39 family protein	F:hydrolase activity;P:unknown;C:unknown;MFPOB	O.I.	C.G.	H.G.
21.5	99.6	22.1	At3g19350	821469	MPC (MATERNALLY EXPRESSED PAB C-TERMINAL)	Encodes a the C-terminal domain of poly(A) binding proteins. MPC is imprinted such that only the maternal allele is expressed in the endosperm. MPC is silenced by the action of MET1 and its expression is promoted by DEM.	O.I.	C.G.	H.G.
19.6	99.6	26.6	At1g28610	839761	GDSL-motif lipase, putative	F:lipase activity, hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBM	O.I.	C.G.	H.G.
19.5	99.6	19.4	At1g52770	841710	phototropic-responsive NPH3 family protein	F:signal transducer activity;P:response to light stimulus;C:cellular_component unknown;P	O.I.	C.G.	H.G.
19.2	99.6	10.1	At2g22920	816823	serine carboxypeptidase S10 family protein	F:serine-type carboxypeptidase activity;P:proteolysis;C:plant-type cell wall;PMFBO	O.I.	C.G.	H.G.
19.0	99.5	123.9	At2g40750	818670	WRKY54	member of WRKY Transcription Factor; Group III	O.I.	C.G.	H.G.
18.1	99.5	13.1	At4g29610	829082	cytidine deaminase, putative / cytidine aminohydrolase, putative	F:hydrolase activity, cytidine deaminase activity, zinc ion binding, catalytic activity;P:cytidine deamination, cytidine metabolic process;C:cellular_component unknown;BOMPFA	O.I.	C.G.	H.G.
17.8	99.5	80.1	At1g13470	837907	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	C.G.	H.G.
17.7	99.5	13.3	At2g47570	819370	60S ribosomal protein L18 (RPL18A)	F:structural constituent of ribosome;P:translation;C:cytosolic large ribosomal subunit, large ribosomal subunit;MOFPA	O.I.	C.G.	H.G.
15.8	99.5	74.6	At5g42900	834301	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
15.6	99.5	17.2	At1g59620	842252	CW9	Encodes CW9.	O.I.	C.G.	H.G.
15.3	99.4	12.7	At5g24480	832519	beta-galactosidase	F:beta-galactosidase activity;P:carbohydrate metabolic process;C:beta-galactosidase complex;P	O.I.	C.G.	H.G.
15.0	99.4	37.6	At3g07650	819956	COL9 (CONSTANS-LIKE 9)	This gene belongs to the CO (CONSTANS) gene family. This gene family is divided in three subgroups: groups III, to which COL9 belongs, is characterised by one B-box (supposed to regulate protein-protein interactions) and a second diverged zinc finger. COL9 downregulates expression of CO (CONSTANS) as well as FT and SOC1 which are known regulatory targets of CO.	O.I.	C.G.	H.G.
13.4	99.4	25.0	At3g04650	819623	oxidoreductase	F:oxidoreductase activity;P:unknown;C:chloroplast;OBPAMF	O.I.	C.G.	H.G.
13.0	99.4	14.7	At5g61290	836250	flavin-containing monooxygenase family protein / FMO family protein	F:NADP or NADPH binding, monooxygenase activity, FAD binding, flavin-containing monooxygenase activity;P:unknown;C:cellular_component unknown;BOMFPA	O.I.	C.G.	H.G.
12.8	99.3	45.2	At4g37150	829869	MES9 (METHYL ESTERASE 9)	Encodes a protein shown to have carboxylesterase activity, methyl salicylate esterase activity, methyl jasmonate esterase activity, and methyl IAA esterase activity in vitro. MES9 appears to be involved in MeSA hydrolysis in planta. Expression of MES9 can restore systemic acquired resistance in SAR-deficient tobacco plants. This protein does not act on MeGA4, or MEGA9 in vitro.	O.I.	C.G.	H.G.
12.7	99.3	76.1	At5g10180	830882	AST68	Encodes a low-affinity sulfate transporter expressed in the root cap and central cylinder, where it is induced by sulfur starvation. Expression in the shoot vascular system is not induced by sulfur starvation.	O.I.	C.G.	H.G.
12.2	99.3	6.3	At5g18880	832006	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
11.7	99.3	73.2	At2g22980	816829	serine-type carboxypeptidase	F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFBO	O.I.	C.G.	H.G.
10.6	99.2	36.6	At5g50450	835113	zinc finger (MYND type) family protein	F:binding, zinc ion binding;P:biological_process unknown;C:cellular_component unknown;FPBMO	O.I.	C.G.	H.G.
10.5	99.2	29.5	At5g38290	833811	peptidyl-tRNA hydrolase family protein	F:aminoacyl-tRNA hydrolase activity;P:translation;C:chloroplast;BOPFM	O.I.	C.G.	H.G.
10.4	99.2	19.9	At3g21950	821753	methyltransferase	F:methyltransferase activity;P:response to cadmium ion;C:cellular_component unknown;POBMF	O.I.	C.G.	H.G.
10.3	99.2	135.9	At1g70890	843427	MLP43 (MLP-LIKE PROTEIN 43)	F:molecular_function unknown;P:response to biotic stimulus, defense response;C:chloroplast;P	O.I.	C.G.	H.G.
10.2	99.2	69.0	At5g52540	835330	unknown protein	F:unknown;P:unknown;C:chloroplast envelope;BOPA	O.I.	C.G.	H.G.
10.2	99.2	34.0	At1g07050	837216	CONSTANS-like protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POF	O.I.	C.G.	H.G.
10.1	99.2	5.0	At5g28560	832953	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:vacuole	O.I.	C.G.	H.G.
9.8	99.1	160.9	At1g21250	838721	WAK1 (CELL WALL-ASSOCIATED KINASE)	cell wall-associated kinase, may function as a signaling receptor of extracellular matrix component.	O.I.	C.G.	H.G.
9.7	99.1	133.6	At5g54960	835587	PDC2 (pyruvate decarboxylase-2)	pyruvate decarboxylase-2	O.I.	C.G.	H.G.
9.7	99.1	9.4	At3g25020	822093	AtRLP42 (Receptor Like Protein 42)	F:protein binding;P:signal transduction, defense response;C:endomembrane system;PMOBFAV	O.I.	C.G.	H.G.
9.5	99.1	24.0	At5g48250	834878	zinc finger (B-box type) family protein	F:transcription factor activity, zinc ion binding;P:unknown;C:plasma membrane;POM	O.I.	C.G.	H.G.
9.4	99.1	9.1	At1g17665	838343	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;OPMF	O.I.	C.G.	H.G.
9.3	99.1	48.0	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.
9.1	99.1	23.2	At5g60100	836132	APRR3 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 3)	Encodes pseudo-response regulator 3 (APRR3/PRR3). PRR3 transcript levels vary in a circadian pattern with peak expression at dusk under long and short day conditions. PRR3 affects the period of the circadian clock and seedlings with reduced levels of PRR3 have shorter periods, based on transcriptional assays of clock-regulated genes. PRR3 is expressed in the vasculature of cotyledons and leaves where it may help stabilize the TOC1 protein by preventing interactions between TOC1 and the F-box protein ZTL.	O.I.	C.G.	H.G.
9.0	99.1	8.7	At2g30420	817593	ETC2	In a tandem repeat with AT2G30424 and AT2G30432	O.I.	C.G.	H.G.
8.8	99.0	102.3	At5g63780	836498	SHA1 (shoot apical meristem arrest 1)	Encodes SHA1 (shoot apical meristem arrest), a putative E3 ligase (a RING finger protein) required for post-embryonic SAM maintenance. The mutant sha1-1 shows a primary SAM-deficient phenotype at the adult stage.	O.I.	C.G.	H.G.
8.8	99.0	21.5	At2g24120	816946	SCA3 (SCABRA 3)	F:DNA-directed RNA polymerase activity, DNA binding;P:transcription;C:mitochondrion;OFPMVB	O.I.	C.G.	H.G.
8.7	99.0	33.0	At3g03090	821117	AtVGT1 (Arabidopsis thaliana vacuolar glucose transporter 1)	Encodes a vacuolar membrane-localized glucose transporter that can also transport fructose. Mutations in these gene have effects on seed germination and time to flowering.	O.I.	C.G.	H.G.

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GSM ID	GSM134366
Assay name	St.Clair_1-27_449_Cvi-1_0.02%-silwet_Rep3_ATH1
GSE experiment	GSE5753: Expression Level Polymorphism Project (ELP) - Cvi-1

Microarray experiments to specifically-expressed genes

GSM ID GSM134366 Assay name St.Clair_1-27_449_Cvi-1_0.02%-silwet_Rep3_ATH1 GSE experiment GSE5753: Expression Level Polymorphism Project (ELP) - Cvi-1

GSM ID GSM134366

Assay name St.Clair_1-27_449_Cvi-1_0.02%-silwet_Rep3_ATH1

GSE experiment GSE5753: Expression Level Polymorphism Project (ELP) - Cvi-1