CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM244442

Assay name Arabidopsis wild-type_T0 (not inoculated)_biological rep1_exp1

GSE experiment GSE9674: Expression data from Arabidopsis plants misexpressing AtMYB30 after Xanthomonas inoculation at early timepoints

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
228.5 100.0 64.1 At3g28320 822460 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBO O.I. C.G. H.G.
201.9 100.0 48.2 At3g28310 822458 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
28.2 99.7 47.1 At1g08890 837410 sugar transporter family protein F:carbohydrate transmembrane transporter activity, sugar:hydrogen symporter activity;P:transport, transmembrane transport;C:chloroplast, membrane;MFBPOA O.I. C.G. H.G.
27.5 99.7 75.5 At1g02300 839576 cathepsin B-like cysteine protease, putative F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis, regulation of catalytic activity;C:endomembrane system;MOPVBAF O.I. C.G. H.G.
19.6 99.6 180.2 At1g29395 839815 COR414-TM1 encodes a protein similar to the cold acclimation protein WCOR413 in wheat. Expression is induced by short-term cold-treatment, water deprivation, and abscisic acid treatment. Possibly targeted to thylakoid membrane. O.I. C.G. H.G.
19.2 99.6 34.6 At1g78450 844181 SOUL heme-binding family protein F:binding;P:biological_process unknown;C:endomembrane system;OMPBA O.I. C.G. H.G.
18.0 99.5 52.3 At1g78070 844142 - F:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;PFO O.I. C.G. H.G.
17.4 99.5 32.1 At1g12710 837826 AtPP2-A12 (Phloem protein 2-A12) This gene is predicted to encode a protein with a PP2 domain. This domain in present in lectins found in squash and cucumber, suggesting that this protein could potentially have carbohydrate binding capabilities. O.I. C.G. H.G.
16.2 99.5 227.0 At4g32340 829368 - F:unknown;P:unknown;C:unknown;MPBOFVA O.I. C.G. H.G.
15.7 99.5 79.3 At1g50290 841451 unknown protein F:molecular_function unknown;P:response to oxidative stress;C:cytosol;P O.I. C.G. H.G.
15.1 99.4 21.7 At5g52910 835368 ATIM (TIMELESS) homolog of Drosophila timeless O.I. C.G. H.G.
14.7 99.4 76.6 At1g20190 838608 ATEXPA11 (ARABIDOPSIS THALIANA EXPANSIN 11) 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.
12.8 99.3 49.4 At2g43010 818903 PIF4 (phytochrome interacting factor 4) Isolated as a semidominant mutation defective in red -light responses. Encodes a nuclear localized bHLH protein that interacts with active PhyB protein. Negatively regulates phyB mediated red light responses. Involved in shade avoidance response. Protein abundance is negatively regulated by PhyB. O.I. C.G. H.G.
12.8 99.3 45.0 At5g27930 832860 protein phosphatase 2C, putative / PP2C, putative F:protein serine/threonine phosphatase activity, catalytic activity;P:biological_process unknown;C:cellular_component unknown;PMOFVB O.I. C.G. H.G.
12.5 99.3 304.2 At5g52310 835307 LTI78 (LOW-TEMPERATURE-INDUCED 78) cold regulated gene, the 5' region of cor78 has cis-acting regulatory elements that can impart cold-regulated gene expression O.I. C.G. H.G.
12.4 99.3 111.0 At5g27280 832786 zinc finger (DNL type) family protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;MFPO O.I. C.G. H.G.
12.2 99.3 133.2 At5g62720 836393 integral membrane HPP family protein F:molecular_function unknown;P:biological_process unknown;C:integral to membrane, chloroplast inner membrane, chloroplast envelope;OBFP O.I. C.G. H.G.
11.9 99.3 24.2 At3g01490 821136 protein kinase, putative F:protein serine/threonine/tyrosine kinase activity, kinase activity;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA O.I. C.G. H.G.
11.7 99.3 59.1 At5g02810 831793 PRR7 (PSEUDO-RESPONSE REGULATOR 7) PRR7 and PRR9 are partially redundant essential components of a temperature-sensitive circadian system. CCA1 and LHY had a positive effect on PRR7 expression levels. O.I. C.G. H.G.
11.5 99.3 410.5 At4g35770 829730 SEN1 (SENESCENCE 1) Senescence-associated gene that is strongly induced by phosphate starvation. Transcripts are differentially regulated at the level of mRNA stability at different times of day. mRNAs are targets of the mRNA degradation pathway mediated by the downstream (DST) instability determinant. O.I. C.G. H.G.
11.5 99.3 115.9 At4g04340 825754 early-responsive to dehydration protein-related / ERD protein-related F:unknown;P:unknown;C:plasma membrane;FPMOB O.I. C.G. H.G.
11.2 99.2 25.7 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.
10.9 99.2 216.2 At2g42530 818853 COR15B (COLD REGULATED 15B) F:unknown;P:response to cold;C:chloroplast, chloroplast stroma, chloroplast envelope;PBOMF O.I. C.G. H.G.
10.4 99.2 41.4 At1g23080 838916 PIN7 (PIN-FORMED 7) Encodes a novel component of auxin efflux that is located apically in the basal cell and is involved during embryogenesis in setting up the apical-basal axis in the embryo. It is also involved in pattern specification during root development. In roots, it is expressed at lateral and basal membranes of provascular cells in the meristem and elongation zone, whereas in the columella cells it coincides with the PIN3 domain. Plasma membrane-localized PIN proteins mediate a saturable efflux of auxin. PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. The action of PINs in auxin efflux is distinct from PGPs, rate-limiting, specific to auxins and sensitive to auxin transport inhibitors. PINs are directly involved of in catalyzing cellular auxin efflux. O.I. C.G. H.G.
10.1 99.2 70.8 At1g30250 839905 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. C.G. H.G.
10.0 99.2 211.9 At1g06460 837158 ACD32.1 (ALPHA-CRYSTALLIN DOMAIN 32.1) ACD32.1 encodes an alpha-crystallin domain containing protein with homology to small heat shock proteins. O.I. C.G. H.G.
10.0 99.2 65.4 At2g21530 816692 forkhead-associated domain-containing protein / FHA domain-containing protein F:unknown;P:biological_process unknown;C:chloroplast thylakoid membrane, chloroplast stroma, chloroplast;BPOAM O.I. C.G. H.G.
10.0 99.2 64.0 At1g79790 844318 haloacid dehalogenase-like hydrolase family protein F:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast;BOMFPA O.I. C.G. H.G.
9.4 99.1 102.1 At4g04330 825753 unknown protein F:unknown;P:unknown;C:unknown;BPO O.I. C.G. H.G.
9.4 99.1 23.3 At4g17120 - - O.I. C.G. H.G.
9.3 99.1 112.7 At2g40610 818656 ATEXPA8 (ARABIDOPSIS THALIANA EXPANSIN A8) 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.
9.3 99.1 70.9 At1g08550 837377 NPQ1 (NON-PHOTOCHEMICAL QUENCHING 1) Violaxanthin deepoxidase involved in xanthophyll cycle.Two major consequences of the npq1 mutation are the absence of zeaxanthin formation in strong light and the partial inhibition of the quenching of singlet excited chlorophylls in the photosystem II light-harvesting complex O.I. C.G. H.G.
9.1 99.1 287.3 At2g15890 816085 MEE14 (maternal effect embryo arrest 14) F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:chloroplast;PO O.I. C.G. H.G.
9.0 99.1 179.2 At1g10760 837619 SEX1 (STARCH EXCESS 1) Encodes an α-glucan, water dikinase required for starch degradation. Involved in cold-induced freezing tolerance. Mutations that eliminate the GWD protein or affect the dikinase domain of the enzyme dramatically reduce both the amount of phosphate in the amylopectin and the rate of starch degradation. Mature leaves of these mutants accumulate amounts of starch up to seven times greater than those in wild-type leaves. NMR analysis of the mutants, suggests that the gene is specifically involved in the phosphorylation of the glucosyl residues of starch at the C6 position. O.I. C.G. H.G.
8.9 99.0 38.7 At2g23840 816916 HNH endonuclease domain-containing protein F:endonuclease activity, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;OBVPA O.I. C.G. H.G.
8.8 99.0 23.4 At2g41870 818787 remorin family protein F:DNA binding;P:biological_process unknown;C:cellular_component unknown;POMFB 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.
228.5	100.0	64.1	At3g28320	822460	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBO	O.I.	C.G.	H.G.
201.9	100.0	48.2	At3g28310	822458	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
28.2	99.7	47.1	At1g08890	837410	sugar transporter family protein	F:carbohydrate transmembrane transporter activity, sugar:hydrogen symporter activity;P:transport, transmembrane transport;C:chloroplast, membrane;MFBPOA	O.I.	C.G.	H.G.
27.5	99.7	75.5	At1g02300	839576	cathepsin B-like cysteine protease, putative	F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis, regulation of catalytic activity;C:endomembrane system;MOPVBAF	O.I.	C.G.	H.G.
19.6	99.6	180.2	At1g29395	839815	COR414-TM1	encodes a protein similar to the cold acclimation protein WCOR413 in wheat. Expression is induced by short-term cold-treatment, water deprivation, and abscisic acid treatment. Possibly targeted to thylakoid membrane.	O.I.	C.G.	H.G.
19.2	99.6	34.6	At1g78450	844181	SOUL heme-binding family protein	F:binding;P:biological_process unknown;C:endomembrane system;OMPBA	O.I.	C.G.	H.G.
18.0	99.5	52.3	At1g78070	844142	-	F:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;PFO	O.I.	C.G.	H.G.
17.4	99.5	32.1	At1g12710	837826	AtPP2-A12 (Phloem protein 2-A12)	This gene is predicted to encode a protein with a PP2 domain. This domain in present in lectins found in squash and cucumber, suggesting that this protein could potentially have carbohydrate binding capabilities.	O.I.	C.G.	H.G.
16.2	99.5	227.0	At4g32340	829368	-	F:unknown;P:unknown;C:unknown;MPBOFVA	O.I.	C.G.	H.G.
15.7	99.5	79.3	At1g50290	841451	unknown protein	F:molecular_function unknown;P:response to oxidative stress;C:cytosol;P	O.I.	C.G.	H.G.
15.1	99.4	21.7	At5g52910	835368	ATIM (TIMELESS)	homolog of Drosophila timeless	O.I.	C.G.	H.G.
14.7	99.4	76.6	At1g20190	838608	ATEXPA11 (ARABIDOPSIS THALIANA EXPANSIN 11)	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.
12.8	99.3	49.4	At2g43010	818903	PIF4 (phytochrome interacting factor 4)	Isolated as a semidominant mutation defective in red -light responses. Encodes a nuclear localized bHLH protein that interacts with active PhyB protein. Negatively regulates phyB mediated red light responses. Involved in shade avoidance response. Protein abundance is negatively regulated by PhyB.	O.I.	C.G.	H.G.
12.8	99.3	45.0	At5g27930	832860	protein phosphatase 2C, putative / PP2C, putative	F:protein serine/threonine phosphatase activity, catalytic activity;P:biological_process unknown;C:cellular_component unknown;PMOFVB	O.I.	C.G.	H.G.
12.5	99.3	304.2	At5g52310	835307	LTI78 (LOW-TEMPERATURE-INDUCED 78)	cold regulated gene, the 5' region of cor78 has cis-acting regulatory elements that can impart cold-regulated gene expression	O.I.	C.G.	H.G.
12.4	99.3	111.0	At5g27280	832786	zinc finger (DNL type) family protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;MFPO	O.I.	C.G.	H.G.
12.2	99.3	133.2	At5g62720	836393	integral membrane HPP family protein	F:molecular_function unknown;P:biological_process unknown;C:integral to membrane, chloroplast inner membrane, chloroplast envelope;OBFP	O.I.	C.G.	H.G.
11.9	99.3	24.2	At3g01490	821136	protein kinase, putative	F:protein serine/threonine/tyrosine kinase activity, kinase activity;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA	O.I.	C.G.	H.G.
11.7	99.3	59.1	At5g02810	831793	PRR7 (PSEUDO-RESPONSE REGULATOR 7)	PRR7 and PRR9 are partially redundant essential components of a temperature-sensitive circadian system. CCA1 and LHY had a positive effect on PRR7 expression levels.	O.I.	C.G.	H.G.
11.5	99.3	410.5	At4g35770	829730	SEN1 (SENESCENCE 1)	Senescence-associated gene that is strongly induced by phosphate starvation. Transcripts are differentially regulated at the level of mRNA stability at different times of day. mRNAs are targets of the mRNA degradation pathway mediated by the downstream (DST) instability determinant.	O.I.	C.G.	H.G.
11.5	99.3	115.9	At4g04340	825754	early-responsive to dehydration protein-related / ERD protein-related	F:unknown;P:unknown;C:plasma membrane;FPMOB	O.I.	C.G.	H.G.
11.2	99.2	25.7	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.
10.9	99.2	216.2	At2g42530	818853	COR15B (COLD REGULATED 15B)	F:unknown;P:response to cold;C:chloroplast, chloroplast stroma, chloroplast envelope;PBOMF	O.I.	C.G.	H.G.
10.4	99.2	41.4	At1g23080	838916	PIN7 (PIN-FORMED 7)	Encodes a novel component of auxin efflux that is located apically in the basal cell and is involved during embryogenesis in setting up the apical-basal axis in the embryo. It is also involved in pattern specification during root development. In roots, it is expressed at lateral and basal membranes of provascular cells in the meristem and elongation zone, whereas in the columella cells it coincides with the PIN3 domain. Plasma membrane-localized PIN proteins mediate a saturable efflux of auxin. PINs mediate auxin efflux from mammalian and yeast cells without needing additional plant-specific factors. The action of PINs in auxin efflux is distinct from PGPs, rate-limiting, specific to auxins and sensitive to auxin transport inhibitors. PINs are directly involved of in catalyzing cellular auxin efflux.	O.I.	C.G.	H.G.
10.1	99.2	70.8	At1g30250	839905	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	C.G.	H.G.
10.0	99.2	211.9	At1g06460	837158	ACD32.1 (ALPHA-CRYSTALLIN DOMAIN 32.1)	ACD32.1 encodes an alpha-crystallin domain containing protein with homology to small heat shock proteins.	O.I.	C.G.	H.G.
10.0	99.2	65.4	At2g21530	816692	forkhead-associated domain-containing protein / FHA domain-containing protein	F:unknown;P:biological_process unknown;C:chloroplast thylakoid membrane, chloroplast stroma, chloroplast;BPOAM	O.I.	C.G.	H.G.
10.0	99.2	64.0	At1g79790	844318	haloacid dehalogenase-like hydrolase family protein	F:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast;BOMFPA	O.I.	C.G.	H.G.
9.4	99.1	102.1	At4g04330	825753	unknown protein	F:unknown;P:unknown;C:unknown;BPO	O.I.	C.G.	H.G.
9.4	99.1	23.3	At4g17120		-	-	O.I.	C.G.	H.G.
9.3	99.1	112.7	At2g40610	818656	ATEXPA8 (ARABIDOPSIS THALIANA EXPANSIN A8)	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.
9.3	99.1	70.9	At1g08550	837377	NPQ1 (NON-PHOTOCHEMICAL QUENCHING 1)	Violaxanthin deepoxidase involved in xanthophyll cycle.Two major consequences of the npq1 mutation are the absence of zeaxanthin formation in strong light and the partial inhibition of the quenching of singlet excited chlorophylls in the photosystem II light-harvesting complex	O.I.	C.G.	H.G.
9.1	99.1	287.3	At2g15890	816085	MEE14 (maternal effect embryo arrest 14)	F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:chloroplast;PO	O.I.	C.G.	H.G.
9.0	99.1	179.2	At1g10760	837619	SEX1 (STARCH EXCESS 1)	Encodes an α-glucan, water dikinase required for starch degradation. Involved in cold-induced freezing tolerance. Mutations that eliminate the GWD protein or affect the dikinase domain of the enzyme dramatically reduce both the amount of phosphate in the amylopectin and the rate of starch degradation. Mature leaves of these mutants accumulate amounts of starch up to seven times greater than those in wild-type leaves. NMR analysis of the mutants, suggests that the gene is specifically involved in the phosphorylation of the glucosyl residues of starch at the C6 position.	O.I.	C.G.	H.G.
8.9	99.0	38.7	At2g23840	816916	HNH endonuclease domain-containing protein	F:endonuclease activity, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;OBVPA	O.I.	C.G.	H.G.
8.8	99.0	23.4	At2g41870	818787	remorin family protein	F:DNA binding;P:biological_process unknown;C:cellular_component unknown;POMFB	O.I.	C.G.	H.G.

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GSM ID	GSM244442
Assay name	Arabidopsis wild-type_T0 (not inoculated)_biological rep1_exp1
GSE experiment	GSE9674: Expression data from Arabidopsis plants misexpressing AtMYB30 after Xanthomonas inoculation at early timepoints

Microarray experiments to specifically-expressed genes

GSM ID GSM244442 Assay name Arabidopsis wild-type_T0 (not inoculated)_biological rep1_exp1 GSE experiment GSE9674: Expression data from Arabidopsis plants misexpressing AtMYB30 after Xanthomonas inoculation at early timepoints

GSM ID GSM244442

Assay name Arabidopsis wild-type_T0 (not inoculated)_biological rep1_exp1

GSE experiment GSE9674: Expression data from Arabidopsis plants misexpressing AtMYB30 after Xanthomonas inoculation at early timepoints