CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM94011

Assay name S5 third repeat

GSE experiment GSE4113: Arabidopsis plants with altered levels of alternative oxidase

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
65.6 99.8 467.5 At3g22370 821806 AOX1A (ALTERNATIVE OXIDASE 1A) Encodes an isoform of alternative oxidase that is expressed in rosettes, flowers, and root. The alternative oxidase of plant mitochondria transfers electrons from the ubiquinone pool to oxygen without energy conservations. It is regulated through transcriptional control and by pyruvate. Plays a role in shoot acclimation to low temperature. Also is capable of ameliorating reactive oxygen species production when the cytochrome pathway is inhibited. O.I. C.G. H.G.
31.9 99.7 40.4 At2g15020 815991 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
26.4 99.7 53.2 At1g13650 837926 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBPVA O.I. C.G. H.G.
21.0 99.6 147.5 At1g55960 842047 - F:molecular_function unknown;P:biological_process unknown;C:unknown;MPO O.I. C.G. H.G.
19.4 99.6 34.7 At2g41870 818787 remorin family protein F:DNA binding;P:biological_process unknown;C:cellular_component unknown;POMFB O.I. C.G. H.G.
18.4 99.5 125.8 At1g02820 839304 late embryogenesis abundant 3 family protein / LEA3 family protein F:molecular_function unknown;P:embryonic development, response to stress;C:unknown;P O.I. C.G. H.G.
16.4 99.5 163.3 At1g32900 840184 starch synthase, putative F:transferase activity, transferring glycosyl groups;P:biosynthetic process, glucan biosynthetic process;C:chloroplast;PBOAFM O.I. C.G. H.G.
16.0 99.5 159.8 At1g58290 842198 HEMA1 Encodes a protein with glutamyl-tRNA reductase (GluTR) activity, catalyzing the NADPH-dependent reduction of Glu-tRNA(Glu) to glutamate 1-semialdehyde (GSA) with the release of free tRNA(Glu). It is involved in the early steps of chlorophyll biosynthesis. O.I. C.G. H.G.
16.0 99.5 67.6 At4g12980 826910 auxin-responsive protein, putative F:unknown;P:multicellular organismal development;C:membrane;PMFOB O.I. C.G. H.G.
15.8 99.5 49.0 At1g78070 844142 - F:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;PFO O.I. C.G. H.G.
15.3 99.4 249.2 At1g66100 842924 thionin, putative Predicted to encode a PR (pathogenesis-related) protein. Belongs to the plant thionin (PR-13) family with the following members: At1g66100, At5g36910, At1g72260, At2g15010, At1g12663, At1g12660. O.I. C.G. H.G.
14.7 99.4 65.5 At1g70580 843395 AOAT2 (ALANINE-2-OXOGLUTARATE AMINOTRANSFERASE 2) Similar to glutamate-glyoxylate transaminase enzyme encoded by AOAT1 O.I. C.G. H.G.
14.4 99.4 227.5 At4g39800 830139 MIPS1 (MYO-INOSITOL-1-PHOSTPATE SYNTHASE 1) Referred to as MIPS2 in Mitsuhashi et al 2008. myo-inositol-1-phosphate synthase isoform 1.Expressed in leaf, root and silique. Immunolocaliazation experiments with an antibody recognizing MIPS1, MIPS2, and MIPS3 showed endosperm localization. O.I. C.G. H.G.
14.1 99.4 150.2 At1g22850 838890 - F:unknown;P:biological_process unknown;C:chloroplast;BOMPFA O.I. C.G. H.G.
13.9 99.4 93.8 At3g01060 821278 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;BOFP O.I. C.G. H.G.
13.7 99.4 39.8 At5g62430 836364 CDF1 (CYCLING DOF FACTOR 1) Dof-type zinc finger domain-containing protein, similar to H-protein promoter binding factor-2a GI:3386546 from (Arabidopsis thaliana). Represses expression of Constans (CO), a circadian regulator of flowering time. Interacts with LKP2 and FKF1. Expression oscillates under constant light conditions. Mainly expressed in the vasculature of cotyledons, leaves and hypocotyls, but also in stomata. Localized to the nucleus and acts as a repressor of CONSTANS through binding to the Dof binding sites in the CO promoter. Protein gets degraded by FKF1 in the afternoon. O.I. C.G. H.G.
13.5 99.4 99.3 At2g22240 816757 MIPS2 (MYO-INOSITOL-1-PHOSTPATE SYNTHASE 2) Referred to as MIPS1 in Mitsuhashi et al 2008. Myo-inositol-1-phosphate synthase isoform 2. Expressed in leaf, root and silique. Immunolocaliazation experiments with an antibody recognizing MIPS1, MIPS2, and MIPS3 showed endosperm localization. O.I. C.G. H.G.
13.4 99.4 126.7 At1g64860 842794 SIGA (SIGMA FACTOR A) Subunit of chloroplast RNA polymerase, confers the ability to recognize promoter sequences on the core enzyme O.I. C.G. H.G.
13.3 99.4 121.4 At5g24150 832480 SQP1 squalene monooxygenase gene homolog O.I. C.G. H.G.
12.8 99.3 121.1 At4g37760 829932 SQE3 (squalene epoxidase 3) F:squalene monooxygenase activity;P:response to jasmonic acid stimulus, sterol biosynthetic process, response to wounding;C:endomembrane system, integral to membrane;BOFMPA O.I. C.G. H.G.
12.8 99.3 59.2 At1g62250 842522 unknown protein F:unknown;P:unknown;C:chloroplast;P O.I. C.G. H.G.
12.7 99.3 26.5 At1g73870 843723 zinc finger (B-box type) family protein F:transcription factor activity, zinc ion binding;P:regulation of transcription;C:intracellular;PO O.I. C.G. H.G.
12.6 99.3 25.3 At5g22390 832300 unknown protein F:unknown;P:unknown;C:unknown;PMOF O.I. C.G. H.G.
12.5 99.3 122.3 At4g33666 829508 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
12.4 99.3 67.6 At5g24120 832477 SIGE (SIGMA FACTOR E) Encodes a specialized sigma factor that functions in regulation of plastid genes and is responsible for the light-dependent transcription at the psbD LRP. Activation of SIG5 is dependent upon blue light and mediated by cryptochromes. O.I. C.G. H.G.
12.3 99.3 165.3 At5g35970 833589 DNA-binding protein, putative F:DNA binding;P:biological_process unknown;C:chloroplast, chloroplast envelope;BMOFPA O.I. C.G. H.G.
12.3 99.3 88.3 At3g02380 821298 COL2 (constans-like 2) homologous to the flowering-time gene CONSTANS (CO) encoding zinc-finger proteins O.I. C.G. H.G.
12.2 99.3 75.1 At1g07180 837229 NDA1 (ALTERNATIVE NAD(P)H DEHYDROGENASE 1) Internal NAD(P)H dehydrogenase in mitochondria. The predicted protein sequence has high homology with other designated NAD(P)H DHs from microorganisms; the capacity for matrix NAD(P)H oxidation via the rotenone-insensitive pathway is significantly reduced in the Atndi1 mutant plant line; the in vitro translation product of AtNDI1 is imported into isolated mitochondria and located on the inside of the inner membrane. O.I. C.G. H.G.
12.1 99.3 247.0 At5g67030 836838 ABA1 (ABA DEFICIENT 1) Encodes a single copy zeaxanthin epoxidase gene that functions in first step of the biosynthesis of the abiotic stress hormone abscisic acid (ABA). Mutants in this gene are unable to express female sterility in response to beta-aminobutyric acid, as wild type plants do. O.I. C.G. H.G.
12.1 99.3 227.1 At1g73600 843694 methyltransferase/ phosphoethanolamine N-methyltransferase F:methyltransferase activity, phosphoethanolamine N-methyltransferase activity;P:metabolic process;C:unknown;BOFAPMV O.I. C.G. H.G.
11.8 99.3 189.5 At1g62180 842514 APR2 (5'ADENYLYLPHOSPHOSULFATE REDUCTASE 2) encodes a adenosine 5'-phosphosulfate reductase, involved in sulfate assimilation. Is a major effect locus for natural variation of shoot sulfate content in Arabidopsis. O.I. C.G. H.G.
11.6 99.3 84.8 At2g34620 818027 mitochondrial transcription termination factor-related / mTERF-related F:molecular_function unknown;P:biological_process unknown;C:unknown;POM O.I. C.G. H.G.
11.6 99.3 52.5 At3g01550 821114 PPT2 (PHOSPHOENOLPYRUVATE (PEP)/PHOSPHATE TRANSLOCATOR 2) F:antiporter activity, triose-phosphate transmembrane transporter activity;P:triose phosphate transport, transport;C:integral to membrane, chloroplast, membrane;PMFOBA O.I. C.G. H.G.
11.6 99.3 40.1 At4g04850 825822 KEA3 member of Putative potassium transporter family O.I. C.G. H.G.
11.3 99.3 116.5 At5g64940 836618 ATATH13 Encodes a member of ATH subfamily of ATP-binding cassette (ABC) proteins. O.I. C.G. H.G.
11.1 99.2 87.8 At3g47500 823904 CDF3 (CYCLING DOF FACTOR 3) Dof-type zinc finger domain-containing protein, identical to H-protein promoter binding factor-2a GI:3386546 from (Arabidopsis thaliana). Interacts with LKP2 and FKF1, but its overexpression does not change flowering time under short or long day conditions. O.I. C.G. H.G.
10.9 99.2 158.6 At4g19170 827655 NCED4 (NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 4) chloroplast-targeted member of a family of enzymes similar to nine-cis-epoxycarotenoid dioxygenase O.I. C.G. H.G.
10.9 99.2 114.0 At3g14067 820621 subtilase family protein F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:apoplast, plasma membrane, vacuole, plant-type cell wall;BPOFAM O.I. C.G. H.G.
10.7 99.2 58.2 At1g68600 843190 unknown protein F:unknown;P:biological_process unknown;C:cellular_component unknown;BPFO O.I. C.G. H.G.
10.4 99.2 20.0 At1g29720 839850 protein kinase family protein F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA O.I. C.G. H.G.
10.2 99.2 33.7 At1g66130 842927 oxidoreductase N-terminal domain-containing protein F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:unknown;BOFMAP O.I. C.G. H.G.
10.1 99.2 232.5 At4g26850 828792 VTC2 (vitamin c defective 2) Encodes a novel protein involved in ascorbate biosynthesis, which was shown to catalyze the transfer of GMP from GDP-galactose to a variety of hexose-1-phosphate acceptors. Recessive mutation has a reduced amount of vitamin C, lower level of non-photochemical quenching, and reduced rate of conversion of violaxanthin to zeaxanthin in high light. O.I. C.G. H.G.
9.7 99.1 111.5 At1g44446 841029 CH1 (CHLORINA 1) Encodes chlorophyllide a oxygenase which converts chlorophyllide a to chlorophyllide b by catalyzing two successive hydroxylations at the 7-methyl group of chlorophyllide a . Mutants are deficient in pigments that associate with thylakoid membrane proteins, lacking chlorophyll b and light-harvesting proteins of photosystem II. The protein was shown through cross-linking experiments to interact with Toc75, Toc34, Tic40, Tic20 and Tic22. O.I. C.G. H.G.
9.7 99.1 38.1 At1g75100 843847 JAC1 (J-DOMAIN PROTEIN REQUIRED FOR CHLOROPLAST ACCUMULATION RESPONSE 1) Contains a J-domain at the C-terminus which is similar to the J-domain of auxilin, a clathrin-uncoating factor in cow, yeast and worm. Arabidopsis contains 6 other proteins similar to auxilin. Expressed in leaves and stems, but not in roots. Localized in the cytoplasm. Required for the chloroplast accumulation response, but not for the avoidance response. No molecular function known. O.I. C.G. H.G.
9.6 99.1 166.2 At2g42690 818869 lipase, putative F:triacylglycerol lipase activity;P:lipid metabolic process;C:chloroplast;PFOBMV O.I. C.G. H.G.
9.5 99.1 20.1 At5g02180 831862 amino acid transporter family protein F:amino acid transmembrane transporter activity;P:amino acid transport;C:chloroplast, membrane;MPFOBAV O.I. C.G. H.G.
9.3 99.1 10.1 At3g24460 822036 TMS membrane family protein / tumour differentially expressed (TDE) family protein F:unknown;P:unknown;C:membrane;MFPO O.I. C.G. H.G.
9.1 99.1 77.1 At2g20570 816579 GPRI1 (GBF'S PRO-RICH REGION-INTERACTING FACTOR 1) Encodes GLK1, Golden2-like 1, one of a pair of partially redundant nuclear transcription factors that regulate chloroplast development in a cell-autonomous manner. GLK2, Golden2-like 2, is encoded by At5g44190. GLK1 and GLK2 regulate the expression of the photosynthetic apparatus. O.I. C.G. H.G.
9.0 99.1 100.2 At5g58870 836004 ftsh9 (FtsH protease 9) encodes an FtsH protease that is localized to the chloroplast O.I. C.G. H.G.
9.0 99.1 87.0 At5g58140 835926 PHOT2 (PHOTOTROPIN 2) Membrane-bound protein serine/threonine kinase that functions as blue light photoreceptor in redundancy with PHO1. Involved in stomatal opening, chloroplast movement and phototropism. Mediates blue light-induced growth enhancements. PHOT1 and PHOT2 mediate blue light-dependent activation of the plasma membrane H+-ATPase in guard cell protoplasts. PHOT2 possesses two LOV (LOV1 and LOV2, for light-oxygen-voltage-sensing) domains involved in FMN-binding and a C-terminus forming a serine/threonine kinase domain. LOV2 acts as an inhibitor of phototropin kinase in the dark, and light cancels the inhibition through cysteine-FMN adduct formation. LOV1 in contrast acts as an attenuator of photoactivation. Localized to the Golgi apparatus under the induction of blue light. O.I. C.G. H.G.
9.0 99.1 71.4 At2g46830 819296 CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) Encodes a transcriptional repressor that performs overlapping functions with LHY in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis. Binds to the evening element in the promoter of TOC1 and represses TOC1 transcription. CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis. O.I. C.G. H.G.
9.0 99.1 34.9 At3g19720 821509 ARC5 (ACCUMULATION AND REPLICATION OF CHLOROPLAST 5) Encodes a novel chloroplast division protein. Mutants of exhibit defects in chloroplast constriction, have enlarged, dumbbell-shaped chloroplasts. The ARC5 gene product shares similarity with the dynamin family of GTPases, which mediate endocytosis, mitochondrial division, and other organellar fission and fusion events in eukaryotes. Phylogenetic analysis showed that ARC5 is related to a group of dynamin-like proteins unique to plants. A GFP�ARC5 fusion protein localizes to a ring at the chloroplast division site. Chloroplast import and protease protection assays indicate that the ARC5 ring is positioned on the outer surface of the chloroplast. Facilitates separation of the two daughter chloroplasts. O.I. C.G. H.G.
8.9 99.0 95.4 At2g04039 814937 unknown protein F:molecular_function unknown;P:unknown;C:chloroplast;BOP O.I. C.G. H.G.
8.9 99.0 79.4 At3g28270 822453 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMPOAFV O.I. C.G. H.G.
8.9 99.0 38.1 At4g10770 826672 OPT7 (OLIGOPEPTIDE TRANSPORTER 7) oligopeptide transporter O.I. C.G. H.G.
8.8 99.0 279.8 At2g26080 817149 AtGLDP2 (Arabidopsis thaliana glycine decarboxylase P-protein 2) F:glycine dehydrogenase (decarboxylating) activity, ATP binding;P:glycine decarboxylation via glycine cleavage system, glycine metabolic process;C:mitochondrion, glycine cleavage complex, chloroplast, chloroplast envelope;OBFAMP O.I. C.G. H.G.
8.8 99.0 182.8 At1g52870 841720 peroxisomal membrane protein-related F:molecular_function unknown;P:biological_process unknown;C:integral to membrane, chloroplast;MPFO O.I. C.G. H.G.
8.8 99.0 47.3 At5g58770 835991 dehydrodolichyl diphosphate synthase, putative / DEDOL-PP synthase, putative F:dehydrodolichyl diphosphate synthase activity;P:dolichol biosynthetic process;C:chloroplast;OBAFMP O.I. C.G. H.G.
8.7 99.0 240.7 At5g49730 835036 ATFRO6 (FERRIC REDUCTION OXIDASE 6) Encodes a plasma membrane-located ferric chelate reductase. Its mRNA is expressed in green aerial tissues (shoot, flower and cotyledon) in a light- and cell differentiation-specific manner. O.I. C.G. H.G.
8.7 99.0 83.8 At2g29290 817478 tropinone reductase, putative / tropine dehydrogenase, putative F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:unknown;BOMFPAV O.I. C.G. H.G.
8.6 99.0 110.9 At5g15450 831398 CLPB3 (CASEIN LYTIC PROTEINASE B3) Encodes a chloroplast-targeted Hsp101 homologue. Functions as a molecular chaperone involved in plastid differentiation mediating internal thylakoid membrane formation and conferring thermotolerance to chloroplasts during heat stress. APG6 is constitutively expressed in the root tips, the organ boundary region, the reproductive tissues of mature plants where plastids exist as proplastids, and slightly in the stems and leaves. APG6 expression is upregulated in response to heat shock in various organs, but not in response to other abiotic stresses. Apg6 mutants have a pale-green phenotype. O.I. C.G. H.G.
8.6 99.0 66.0 At1g64970 842805 G-TMT (GAMMA-TOCOPHEROL METHYLTRANSFERASE) gamma-tocopherol methyltransferase (g-TMT) mRNA, nuclear; mutant has Deficient in alpha and beta tocopherol; Accumulates gamma tocopherol in leaves 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.
65.6	99.8	467.5	At3g22370	821806	AOX1A (ALTERNATIVE OXIDASE 1A)	Encodes an isoform of alternative oxidase that is expressed in rosettes, flowers, and root. The alternative oxidase of plant mitochondria transfers electrons from the ubiquinone pool to oxygen without energy conservations. It is regulated through transcriptional control and by pyruvate. Plays a role in shoot acclimation to low temperature. Also is capable of ameliorating reactive oxygen species production when the cytochrome pathway is inhibited.	O.I.	C.G.	H.G.
31.9	99.7	40.4	At2g15020	815991	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
26.4	99.7	53.2	At1g13650	837926	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBPVA	O.I.	C.G.	H.G.
21.0	99.6	147.5	At1g55960	842047	-	F:molecular_function unknown;P:biological_process unknown;C:unknown;MPO	O.I.	C.G.	H.G.
19.4	99.6	34.7	At2g41870	818787	remorin family protein	F:DNA binding;P:biological_process unknown;C:cellular_component unknown;POMFB	O.I.	C.G.	H.G.
18.4	99.5	125.8	At1g02820	839304	late embryogenesis abundant 3 family protein / LEA3 family protein	F:molecular_function unknown;P:embryonic development, response to stress;C:unknown;P	O.I.	C.G.	H.G.
16.4	99.5	163.3	At1g32900	840184	starch synthase, putative	F:transferase activity, transferring glycosyl groups;P:biosynthetic process, glucan biosynthetic process;C:chloroplast;PBOAFM	O.I.	C.G.	H.G.
16.0	99.5	159.8	At1g58290	842198	HEMA1	Encodes a protein with glutamyl-tRNA reductase (GluTR) activity, catalyzing the NADPH-dependent reduction of Glu-tRNA(Glu) to glutamate 1-semialdehyde (GSA) with the release of free tRNA(Glu). It is involved in the early steps of chlorophyll biosynthesis.	O.I.	C.G.	H.G.
16.0	99.5	67.6	At4g12980	826910	auxin-responsive protein, putative	F:unknown;P:multicellular organismal development;C:membrane;PMFOB	O.I.	C.G.	H.G.
15.8	99.5	49.0	At1g78070	844142	-	F:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;PFO	O.I.	C.G.	H.G.
15.3	99.4	249.2	At1g66100	842924	thionin, putative	Predicted to encode a PR (pathogenesis-related) protein. Belongs to the plant thionin (PR-13) family with the following members: At1g66100, At5g36910, At1g72260, At2g15010, At1g12663, At1g12660.	O.I.	C.G.	H.G.
14.7	99.4	65.5	At1g70580	843395	AOAT2 (ALANINE-2-OXOGLUTARATE AMINOTRANSFERASE 2)	Similar to glutamate-glyoxylate transaminase enzyme encoded by AOAT1	O.I.	C.G.	H.G.
14.4	99.4	227.5	At4g39800	830139	MIPS1 (MYO-INOSITOL-1-PHOSTPATE SYNTHASE 1)	** Referred to as MIPS2 in Mitsuhashi et al 2008. myo-inositol-1-phosphate synthase isoform 1.Expressed in leaf, root and silique. Immunolocaliazation experiments with an antibody recognizing MIPS1, MIPS2, and MIPS3 showed endosperm localization.	O.I.	C.G.	H.G.
14.1	99.4	150.2	At1g22850	838890	-	F:unknown;P:biological_process unknown;C:chloroplast;BOMPFA	O.I.	C.G.	H.G.
13.9	99.4	93.8	At3g01060	821278	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;BOFP	O.I.	C.G.	H.G.
13.7	99.4	39.8	At5g62430	836364	CDF1 (CYCLING DOF FACTOR 1)	Dof-type zinc finger domain-containing protein, similar to H-protein promoter binding factor-2a GI:3386546 from (Arabidopsis thaliana). Represses expression of Constans (CO), a circadian regulator of flowering time. Interacts with LKP2 and FKF1. Expression oscillates under constant light conditions. Mainly expressed in the vasculature of cotyledons, leaves and hypocotyls, but also in stomata. Localized to the nucleus and acts as a repressor of CONSTANS through binding to the Dof binding sites in the CO promoter. Protein gets degraded by FKF1 in the afternoon.	O.I.	C.G.	H.G.
13.5	99.4	99.3	At2g22240	816757	MIPS2 (MYO-INOSITOL-1-PHOSTPATE SYNTHASE 2)	** Referred to as MIPS1 in Mitsuhashi et al 2008. Myo-inositol-1-phosphate synthase isoform 2. Expressed in leaf, root and silique. Immunolocaliazation experiments with an antibody recognizing MIPS1, MIPS2, and MIPS3 showed endosperm localization.	O.I.	C.G.	H.G.
13.4	99.4	126.7	At1g64860	842794	SIGA (SIGMA FACTOR A)	Subunit of chloroplast RNA polymerase, confers the ability to recognize promoter sequences on the core enzyme	O.I.	C.G.	H.G.
13.3	99.4	121.4	At5g24150	832480	SQP1	squalene monooxygenase gene homolog	O.I.	C.G.	H.G.
12.8	99.3	121.1	At4g37760	829932	SQE3 (squalene epoxidase 3)	F:squalene monooxygenase activity;P:response to jasmonic acid stimulus, sterol biosynthetic process, response to wounding;C:endomembrane system, integral to membrane;BOFMPA	O.I.	C.G.	H.G.
12.8	99.3	59.2	At1g62250	842522	unknown protein	F:unknown;P:unknown;C:chloroplast;P	O.I.	C.G.	H.G.
12.7	99.3	26.5	At1g73870	843723	zinc finger (B-box type) family protein	F:transcription factor activity, zinc ion binding;P:regulation of transcription;C:intracellular;PO	O.I.	C.G.	H.G.
12.6	99.3	25.3	At5g22390	832300	unknown protein	F:unknown;P:unknown;C:unknown;PMOF	O.I.	C.G.	H.G.
12.5	99.3	122.3	At4g33666	829508	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
12.4	99.3	67.6	At5g24120	832477	SIGE (SIGMA FACTOR E)	Encodes a specialized sigma factor that functions in regulation of plastid genes and is responsible for the light-dependent transcription at the psbD LRP. Activation of SIG5 is dependent upon blue light and mediated by cryptochromes.	O.I.	C.G.	H.G.
12.3	99.3	165.3	At5g35970	833589	DNA-binding protein, putative	F:DNA binding;P:biological_process unknown;C:chloroplast, chloroplast envelope;BMOFPA	O.I.	C.G.	H.G.
12.3	99.3	88.3	At3g02380	821298	COL2 (constans-like 2)	homologous to the flowering-time gene CONSTANS (CO) encoding zinc-finger proteins	O.I.	C.G.	H.G.
12.2	99.3	75.1	At1g07180	837229	NDA1 (ALTERNATIVE NAD(P)H DEHYDROGENASE 1)	Internal NAD(P)H dehydrogenase in mitochondria. The predicted protein sequence has high homology with other designated NAD(P)H DHs from microorganisms; the capacity for matrix NAD(P)H oxidation via the rotenone-insensitive pathway is significantly reduced in the Atndi1 mutant plant line; the in vitro translation product of AtNDI1 is imported into isolated mitochondria and located on the inside of the inner membrane.	O.I.	C.G.	H.G.
12.1	99.3	247.0	At5g67030	836838	ABA1 (ABA DEFICIENT 1)	Encodes a single copy zeaxanthin epoxidase gene that functions in first step of the biosynthesis of the abiotic stress hormone abscisic acid (ABA). Mutants in this gene are unable to express female sterility in response to beta-aminobutyric acid, as wild type plants do.	O.I.	C.G.	H.G.
12.1	99.3	227.1	At1g73600	843694	methyltransferase/ phosphoethanolamine N-methyltransferase	F:methyltransferase activity, phosphoethanolamine N-methyltransferase activity;P:metabolic process;C:unknown;BOFAPMV	O.I.	C.G.	H.G.
11.8	99.3	189.5	At1g62180	842514	APR2 (5'ADENYLYLPHOSPHOSULFATE REDUCTASE 2)	encodes a adenosine 5'-phosphosulfate reductase, involved in sulfate assimilation. Is a major effect locus for natural variation of shoot sulfate content in Arabidopsis.	O.I.	C.G.	H.G.
11.6	99.3	84.8	At2g34620	818027	mitochondrial transcription termination factor-related / mTERF-related	F:molecular_function unknown;P:biological_process unknown;C:unknown;POM	O.I.	C.G.	H.G.
11.6	99.3	52.5	At3g01550	821114	PPT2 (PHOSPHOENOLPYRUVATE (PEP)/PHOSPHATE TRANSLOCATOR 2)	F:antiporter activity, triose-phosphate transmembrane transporter activity;P:triose phosphate transport, transport;C:integral to membrane, chloroplast, membrane;PMFOBA	O.I.	C.G.	H.G.
11.6	99.3	40.1	At4g04850	825822	KEA3	member of Putative potassium transporter family	O.I.	C.G.	H.G.
11.3	99.3	116.5	At5g64940	836618	ATATH13	Encodes a member of ATH subfamily of ATP-binding cassette (ABC) proteins.	O.I.	C.G.	H.G.
11.1	99.2	87.8	At3g47500	823904	CDF3 (CYCLING DOF FACTOR 3)	Dof-type zinc finger domain-containing protein, identical to H-protein promoter binding factor-2a GI:3386546 from (Arabidopsis thaliana). Interacts with LKP2 and FKF1, but its overexpression does not change flowering time under short or long day conditions.	O.I.	C.G.	H.G.
10.9	99.2	158.6	At4g19170	827655	NCED4 (NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 4)	chloroplast-targeted member of a family of enzymes similar to nine-cis-epoxycarotenoid dioxygenase	O.I.	C.G.	H.G.
10.9	99.2	114.0	At3g14067	820621	subtilase family protein	F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:apoplast, plasma membrane, vacuole, plant-type cell wall;BPOFAM	O.I.	C.G.	H.G.
10.7	99.2	58.2	At1g68600	843190	unknown protein	F:unknown;P:biological_process unknown;C:cellular_component unknown;BPFO	O.I.	C.G.	H.G.
10.4	99.2	20.0	At1g29720	839850	protein kinase family protein	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA	O.I.	C.G.	H.G.
10.2	99.2	33.7	At1g66130	842927	oxidoreductase N-terminal domain-containing protein	F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:unknown;BOFMAP	O.I.	C.G.	H.G.
10.1	99.2	232.5	At4g26850	828792	VTC2 (vitamin c defective 2)	Encodes a novel protein involved in ascorbate biosynthesis, which was shown to catalyze the transfer of GMP from GDP-galactose to a variety of hexose-1-phosphate acceptors. Recessive mutation has a reduced amount of vitamin C, lower level of non-photochemical quenching, and reduced rate of conversion of violaxanthin to zeaxanthin in high light.	O.I.	C.G.	H.G.
9.7	99.1	111.5	At1g44446	841029	CH1 (CHLORINA 1)	Encodes chlorophyllide a oxygenase which converts chlorophyllide a to chlorophyllide b by catalyzing two successive hydroxylations at the 7-methyl group of chlorophyllide a . Mutants are deficient in pigments that associate with thylakoid membrane proteins, lacking chlorophyll b and light-harvesting proteins of photosystem II. The protein was shown through cross-linking experiments to interact with Toc75, Toc34, Tic40, Tic20 and Tic22.	O.I.	C.G.	H.G.
9.7	99.1	38.1	At1g75100	843847	JAC1 (J-DOMAIN PROTEIN REQUIRED FOR CHLOROPLAST ACCUMULATION RESPONSE 1)	Contains a J-domain at the C-terminus which is similar to the J-domain of auxilin, a clathrin-uncoating factor in cow, yeast and worm. Arabidopsis contains 6 other proteins similar to auxilin. Expressed in leaves and stems, but not in roots. Localized in the cytoplasm. Required for the chloroplast accumulation response, but not for the avoidance response. No molecular function known.	O.I.	C.G.	H.G.
9.6	99.1	166.2	At2g42690	818869	lipase, putative	F:triacylglycerol lipase activity;P:lipid metabolic process;C:chloroplast;PFOBMV	O.I.	C.G.	H.G.
9.5	99.1	20.1	At5g02180	831862	amino acid transporter family protein	F:amino acid transmembrane transporter activity;P:amino acid transport;C:chloroplast, membrane;MPFOBAV	O.I.	C.G.	H.G.
9.3	99.1	10.1	At3g24460	822036	TMS membrane family protein / tumour differentially expressed (TDE) family protein	F:unknown;P:unknown;C:membrane;MFPO	O.I.	C.G.	H.G.
9.1	99.1	77.1	At2g20570	816579	GPRI1 (GBF'S PRO-RICH REGION-INTERACTING FACTOR 1)	Encodes GLK1, Golden2-like 1, one of a pair of partially redundant nuclear transcription factors that regulate chloroplast development in a cell-autonomous manner. GLK2, Golden2-like 2, is encoded by At5g44190. GLK1 and GLK2 regulate the expression of the photosynthetic apparatus.	O.I.	C.G.	H.G.
9.0	99.1	100.2	At5g58870	836004	ftsh9 (FtsH protease 9)	encodes an FtsH protease that is localized to the chloroplast	O.I.	C.G.	H.G.
9.0	99.1	87.0	At5g58140	835926	PHOT2 (PHOTOTROPIN 2)	Membrane-bound protein serine/threonine kinase that functions as blue light photoreceptor in redundancy with PHO1. Involved in stomatal opening, chloroplast movement and phototropism. Mediates blue light-induced growth enhancements. PHOT1 and PHOT2 mediate blue light-dependent activation of the plasma membrane H+-ATPase in guard cell protoplasts. PHOT2 possesses two LOV (LOV1 and LOV2, for light-oxygen-voltage-sensing) domains involved in FMN-binding and a C-terminus forming a serine/threonine kinase domain. LOV2 acts as an inhibitor of phototropin kinase in the dark, and light cancels the inhibition through cysteine-FMN adduct formation. LOV1 in contrast acts as an attenuator of photoactivation. Localized to the Golgi apparatus under the induction of blue light.	O.I.	C.G.	H.G.
9.0	99.1	71.4	At2g46830	819296	CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)	Encodes a transcriptional repressor that performs overlapping functions with LHY in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis. Binds to the evening element in the promoter of TOC1 and represses TOC1 transcription. CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.	O.I.	C.G.	H.G.
9.0	99.1	34.9	At3g19720	821509	ARC5 (ACCUMULATION AND REPLICATION OF CHLOROPLAST 5)	Encodes a novel chloroplast division protein. Mutants of exhibit defects in chloroplast constriction, have enlarged, dumbbell-shaped chloroplasts. The ARC5 gene product shares similarity with the dynamin family of GTPases, which mediate endocytosis, mitochondrial division, and other organellar fission and fusion events in eukaryotes. Phylogenetic analysis showed that ARC5 is related to a group of dynamin-like proteins unique to plants. A GFP�ARC5 fusion protein localizes to a ring at the chloroplast division site. Chloroplast import and protease protection assays indicate that the ARC5 ring is positioned on the outer surface of the chloroplast. Facilitates separation of the two daughter chloroplasts.	O.I.	C.G.	H.G.
8.9	99.0	95.4	At2g04039	814937	unknown protein	F:molecular_function unknown;P:unknown;C:chloroplast;BOP	O.I.	C.G.	H.G.
8.9	99.0	79.4	At3g28270	822453	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMPOAFV	O.I.	C.G.	H.G.
8.9	99.0	38.1	At4g10770	826672	OPT7 (OLIGOPEPTIDE TRANSPORTER 7)	oligopeptide transporter	O.I.	C.G.	H.G.
8.8	99.0	279.8	At2g26080	817149	AtGLDP2 (Arabidopsis thaliana glycine decarboxylase P-protein 2)	F:glycine dehydrogenase (decarboxylating) activity, ATP binding;P:glycine decarboxylation via glycine cleavage system, glycine metabolic process;C:mitochondrion, glycine cleavage complex, chloroplast, chloroplast envelope;OBFAMP	O.I.	C.G.	H.G.
8.8	99.0	182.8	At1g52870	841720	peroxisomal membrane protein-related	F:molecular_function unknown;P:biological_process unknown;C:integral to membrane, chloroplast;MPFO	O.I.	C.G.	H.G.
8.8	99.0	47.3	At5g58770	835991	dehydrodolichyl diphosphate synthase, putative / DEDOL-PP synthase, putative	F:dehydrodolichyl diphosphate synthase activity;P:dolichol biosynthetic process;C:chloroplast;OBAFMP	O.I.	C.G.	H.G.
8.7	99.0	240.7	At5g49730	835036	ATFRO6 (FERRIC REDUCTION OXIDASE 6)	Encodes a plasma membrane-located ferric chelate reductase. Its mRNA is expressed in green aerial tissues (shoot, flower and cotyledon) in a light- and cell differentiation-specific manner.	O.I.	C.G.	H.G.
8.7	99.0	83.8	At2g29290	817478	tropinone reductase, putative / tropine dehydrogenase, putative	F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:unknown;BOMFPAV	O.I.	C.G.	H.G.
8.6	99.0	110.9	At5g15450	831398	CLPB3 (CASEIN LYTIC PROTEINASE B3)	Encodes a chloroplast-targeted Hsp101 homologue. Functions as a molecular chaperone involved in plastid differentiation mediating internal thylakoid membrane formation and conferring thermotolerance to chloroplasts during heat stress. APG6 is constitutively expressed in the root tips, the organ boundary region, the reproductive tissues of mature plants where plastids exist as proplastids, and slightly in the stems and leaves. APG6 expression is upregulated in response to heat shock in various organs, but not in response to other abiotic stresses. Apg6 mutants have a pale-green phenotype.	O.I.	C.G.	H.G.
8.6	99.0	66.0	At1g64970	842805	G-TMT (GAMMA-TOCOPHEROL METHYLTRANSFERASE)	gamma-tocopherol methyltransferase (g-TMT) mRNA, nuclear; mutant has Deficient in alpha and beta tocopherol; Accumulates gamma tocopherol in leaves	O.I.	C.G.	H.G.

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GSM ID	GSM94011
Assay name	S5 third repeat
GSE experiment	GSE4113: Arabidopsis plants with altered levels of alternative oxidase

Microarray experiments to specifically-expressed genes

GSM ID GSM94011 Assay name S5 third repeat GSE experiment GSE4113: Arabidopsis plants with altered levels of alternative oxidase

GSM ID GSM94011

Assay name S5 third repeat

GSE experiment GSE4113: Arabidopsis plants with altered levels of alternative oxidase