CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM128793

Assay name Zarka_1-5_MT-WT24HA_Rep1_ATH1

GSE experiment GSE5534: Response to cold, plate grown plants

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
105.6 99.9 230.2 At1g09350 837457 AtGolS3 (Arabidopsis thaliana galactinol synthase 3) F:transferase activity, transferring hexosyl groups, transferase activity, transferring glycosyl groups;P:carbohydrate biosynthetic process;C:cellular_component unknown;PMFVBO O.I. C.G. H.G.
39.2 99.8 469.1 At4g17090 827419 CT-BMY (CHLOROPLAST BETA-AMYLASE) Encodes a beta-amylase targeted to the chloroplast. Transgenic BMY8 RNAi lines fail to accumulate maltose during cold shock suggesting that maltose accumulation coincides with BMY8 expression. Apart from maltose, the sugar content of the RNAi lines were similar to wildtype (glucose and sucrose unaffected). O.I. C.G. H.G.
38.1 99.8 27.0 At3g55580 824723 regulator of chromosome condensation (RCC1) family protein F:binding;P:biological_process unknown;C:cellular_component unknown;MOBPFAV O.I. C.G. H.G.
27.8 99.7 26.7 At2g22590 816790 transferase, transferring glycosyl groups F:transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBFOV O.I. C.G. H.G.
23.8 99.6 489.0 At3g50970 824261 LTI30 (LOW TEMPERATURE-INDUCED 30) Belongs to the dehydrin protein family, which contains highly conserved stretches of 7-17 residues that are repetitively scattered in their sequences, the K-, S-, Y- and lysine rich segments. LTI29 and LTI30 double overexpressors confer freeze tolerance. Located in membranes. mRNA upregulated by water deprivation and abscisic acid. O.I. C.G. H.G.
23.8 99.6 68.6 At2g35960 818169 NHL12 Encodes a protein whose sequence is similar to tobacco hairpin-induced gene (HIN1) and Arabidopsis non-race specific disease resistance gene (NDR1). Expression is not altered in response to cucumber mosaic virus or spermine. O.I. C.G. H.G.
22.9 99.6 66.3 At4g03400 827938 DFL2 (DWARF IN LIGHT 2) Encodes a GH3-related gene involved in red light-specific hypocotyl elongation. Analysis of sense and antisense transgenic plants suggests that DFL2 is located downstream of red light signal transduction and determines the degree of hypocotyl elongation. O.I. C.G. H.G.
22.6 99.6 105.9 At4g27560 828865 glycosyltransferase family protein F:transferase activity, transferring glycosyl groups;P:response to salt stress, N-terminal protein myristoylation;C:cellular_component unknown;PMBFOV O.I. C.G. H.G.
22.3 99.6 116.7 At5g57110 835815 ACA8 (AUTOINHIBITED CA2+ -ATPASE, ISOFORM 8) Arabidopsis-autoinhibited Ca2+ -ATPase, isoform 8, contains all of the characteristic motifs of Ca2+ -transporting P-type Ca2+ -ATPases and is localized to the plasma membrane. O.I. C.G. H.G.
22.2 99.6 60.1 At4g17550 827470 transporter-related F:sugar:hydrogen symporter activity;P:carbohydrate transport;C:plasma membrane;BMFOPA O.I. C.G. H.G.
22.1 99.6 403.7 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.
19.3 99.6 54.4 At4g34740 829626 ATASE2 (GLN PHOSPHORIBOSYL PYROPHOSPHATE AMIDOTRANSFERASE 2) Encodes glutamine 5-phosphoribosylpyrophosphate amidotransferase. Mutants are deficient in leaf, but not cotyledon, plastid and palisade cell development. Mutants exhibit defective chloroplast development under non-low light, suggesting that the defect in chloroplast development is caused by photo-oxidative damage. O.I. C.G. H.G.
18.8 99.5 43.1 At3g14890 820718 phosphoesterase F:DNA binding, catalytic activity, zinc ion binding;P:unknown;C:unknown;MOFPVBA O.I. C.G. H.G.
18.7 99.5 70.8 At5g24470 832518 APRR5 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5) Encodes a pseudo-response regulator whose mutation affects various circadian-associated biological events such as flowering time in the long-day photoperiod conditions, red light sensitivity of seedlings during early photomorphogenesis, and the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light. O.I. C.G. H.G.
18.6 99.5 82.4 At1g16850 838256 unknown protein F:molecular_function unknown;P:response to salt stress;C:endomembrane system;P O.I. C.G. H.G.
17.2 99.5 168.6 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.
16.4 99.5 264.4 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.
16.1 99.5 240.2 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.
15.8 99.5 98.6 At5g62210 836342 embryo-specific protein-related F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;MPOFVBA O.I. C.G. H.G.
15.7 99.5 46.7 At2g28550 817403 RAP2.7 (RELATED TO AP2.7) F:transcription factor activity, DNA binding;P:organ morphogenesis, regulation of transcription, DNA-dependent, vegetative to reproductive phase transition;C:nucleus;POBV O.I. C.G. H.G.
15.2 99.4 48.3 At1g53035 841737 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
15.1 99.4 197.4 At3g54400 824606 aspartyl protease family protein F:aspartic-type endopeptidase activity;P:proteolysis;C:apoplast, cell wall, chloroplast, plant-type cell wall;PMFO O.I. C.G. H.G.
15.1 99.4 54.0 At4g18390 827568 TCP family transcription factor, putative F:transcription factor activity;P:regulation of transcription;C:cellular_component unknown;POMFB O.I. C.G. H.G.
15.0 99.4 287.9 At2g31360 817694 ADS2 (16:0Delta9 Arabidopsis desaturase 2) homologous to delta 9 acyl-lipid desaturases of cyanobacteria and acyl-CoA desaturases of yeast and mammals. expression up-regulated by cold temperature. O.I. C.G. H.G.
15.0 99.4 27.2 At5g48070 834859 XTH20 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 20) putative xyloglucan endotransglycosylase/hydrolase, expressed primarily in the stele of mature non-elongating regions of both the main and the lateral root. Is expressed in lateral root primordia but expression ceases after lateral root begins to grow. O.I. C.G. H.G.
14.7 99.4 96.3 At3g55120 824678 TT5 (TRANSPARENT TESTA 5) Catalyzes the conversion of chalcones into flavanones. Required for the accumulation of purple anthocyanins in leaves and stems. O.I. C.G. H.G.
14.7 99.4 49.1 At2g21320 816671 zinc finger (B-box type) family protein F:transcription factor activity, zinc ion binding;P:regulation of transcription;C:endomembrane system, intracellular;POM O.I. C.G. H.G.
14.4 99.4 16.3 At1g01420 837503 UGT72B3 (UDP-GLUCOSYL TRANSFERASE 72B3) F:quercetin 3-O-glucosyltransferase activity, UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBVOF O.I. C.G. H.G.
13.5 99.4 45.4 At1g78070 844142 - F:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;PFO O.I. C.G. H.G.
12.8 99.3 68.1 At5g42570 834264 - F:molecular_function unknown;P:intracellular protein transport;C:endoplasmic reticulum, plasma membrane;MPOFAB O.I. C.G. H.G.
12.6 99.3 121.1 At1g80130 844353 binding F:binding;P:response to oxidative stress;C:membrane;BPOMFAV O.I. C.G. H.G.
12.6 99.3 28.6 At4g38400 829997 ATEXLA2 (ARABIDOPSIS THALIANA EXPANSIN-LIKE A2) member of EXPANSIN-LIKE. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio) O.I. C.G. H.G.
12.3 99.3 112.1 At1g62570 842554 FMO GS-OX4 (FLAVIN-MONOOXYGENASE GLUCOSINOLATE S-OXYGENASE 4) belongs to the flavin-monooxygenase (FMO) family, encodes a glucosinolate S-oxygenase that catalyzes the conversion of methylthioalkyl glucosinolates to methylsulfinylalkyl glucosinolates O.I. C.G. H.G.
12.2 99.3 17.8 At4g37320 829887 CYP81D5 member of CYP81D O.I. C.G. H.G.
12.1 99.3 227.2 At4g27520 828861 plastocyanin-like domain-containing protein F:electron carrier activity, copper ion binding;P:unknown;C:in 6 components;MOFBPVA O.I. C.G. H.G.
12.1 99.3 32.5 At3g17130 820970 invertase/pectin methylesterase inhibitor family protein F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:unknown;C:endomembrane system;P O.I. C.G. H.G.
12.0 99.3 408.0 At2g42540 818854 COR15A (COLD-REGULATED 15A) A cold-regulated gene whose product is targeted to the chloroplast and constitutive expression increases freezing tolerance in protoplasts in vitro and chloroplasts in vivo. NMR and x-ray diffraction studies suggest that COR15a alters the intrinsic curvature of the inner membrane of chloroplast envelope. O.I. C.G. H.G.
11.9 99.3 39.9 At1g51610 841586 cation efflux family protein / metal tolerance protein, putative (MTPc4) F:cation transmembrane transporter activity, efflux transmembrane transporter activity;P:cation transport;C:membrane;BOMAP O.I. C.G. H.G.
11.8 99.3 327.4 At2g28900 817439 ATOEP16-1 (OUTER PLASTID ENVELOPE PROTEIN 16-1) Encodes AtOEP16, a 16-KDa plastid outer membrane protein involved in plastid import of protochlorophyllide oxidoreductase A. Predominantly expressed in leaves and is also inducible by cold treatment. O.I. C.G. H.G.
11.7 99.3 131.1 At4g24960 828598 ATHVA22D Homologous to a eukaryote specific ABA- and stress-inducible gene first isolated from barley. Groups in one subfamily with ATHVA22E. Along with other members of the ATHVA22 family, it may be involved in regulation of autophagy during development. O.I. C.G. H.G.
11.4 99.3 26.9 At3g09540 820111 pectate lyase family protein F:lyase activity, pectate lyase activity;P:N-terminal protein myristoylation;C:unknown;BPFO O.I. C.G. H.G.
11.3 99.3 51.7 At1g64890 842797 integral membrane transporter family protein F:transporter activity;P:transport;C:membrane;BOPMAF O.I. C.G. H.G.
11.2 99.2 37.2 At2g24050 816939 MIF4G domain-containing protein / MA3 domain-containing protein F:protein binding, RNA binding, binding;P:translation, RNA metabolic process;C:unknown;MPOFBV O.I. C.G. H.G.
11.0 99.2 47.8 At4g32190 829352 centromeric protein-related F:unknown;P:unknown;C:unknown;MOBFPAV O.I. C.G. H.G.
10.9 99.2 20.5 At3g21540 821708 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:rRNA processing;C:nucleolus, heterotrimeric G-protein complex;MFOPBA O.I. C.G. H.G.
10.7 99.2 78.1 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.
10.7 99.2 77.7 At2g31380 817696 STH a B-box zinc finger protein that interacts with COP1. contains a novel 11 amino acid motif at the C-terminus (also found at the N-terminus of HY5) that is involved in the COP1 interaction. O.I. C.G. H.G.
10.6 99.2 22.0 At5g47650 834816 ATNUDT2 (ARABIDOPSIS THALIANA NUDIX HYDROLASE HOMOLOG 2) Encodes an ADP-ribose pyrophosphatase that confers enhanced tolerance to oxidative stress. O.I. C.G. H.G.
10.5 99.2 47.4 At1g27760 839669 interferon-related developmental regulator family protein / IFRD protein family Encodes a protein with similarity to human interferon-related developmental regulator (IFRD)that is involved in salt tolerance. Loss of function mutations are hypersensitive to salt stress and have reduced fertility. SAT32 is found in the cytoplasm but appears to translocate to the nucleus when plants are subject to salt stress. O.I. C.G. H.G.
10.4 99.2 37.3 At1g49720 841395 ABF1 (ABSCISIC ACID RESPONSIVE ELEMENT-BINDING FACTOR 1) Identified as a protein that binds to abscisic acid response elements. May mediate transcriptional regulation of ABA responses. O.I. C.G. H.G.
10.4 99.2 35.8 At3g10530 820218 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;BMFOPA O.I. C.G. H.G.
10.3 99.2 538.0 At1g20440 838632 COR47 (COLD-REGULATED 47) Belongs to the dehydrin protein family, which contains highly conserved stretches of 7-17 residues that are repetitively scattered in their sequences, the K-, S-, Y- and lysine rich segments. Cold regulated gene, amino acid sequence homology with Group II LEA (late embryogenesis abundant) proteins. Also responds to osmotic stress, ABA, dehydration and inhibits e.coli growth while overexpressed. COR47 and RAB18 double overexpressor plants are cold tolerant. O.I. C.G. H.G.
10.3 99.2 27.4 At1g03530 839468 NAF1 (NUCLEAR ASSEMBLY FACTOR 1) F:unknown;P:biological_process unknown;C:unknown;MOBFPVA O.I. C.G. H.G.
10.2 99.2 33.6 At1g71710 843501 inositol polyphosphate 5-phosphatase, putative F:inositol-polyphosphate 5-phosphatase activity, inositol or phosphatidylinositol phosphatase activity;P:biological_process unknown;C:cellular_component unknown;MFPOV O.I. C.G. H.G.
10.0 99.2 38.3 At1g24530 839068 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:plasma membrane, heterotrimeric G-protein complex;MFOBPA O.I. C.G. H.G.
10.0 99.2 12.1 At3g62690 825443 ATL5 (ATL5) Encodes a RING-H2 zinc finger protein related to ATL2. The ATL gene family is represented by fifteen sequences that contain, in addition to the RING, a transmembrane domain which is located in most of them towards the N-terminal end. O.I. C.G. H.G.
9.8 99.1 23.0 At4g04940 825833 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:rRNA processing;C:CUL4 RING ubiquitin ligase complex;MFBOPA O.I. C.G. H.G.
9.7 99.1 363.7 At4g12470 826859 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein F:lipid binding;P:defense response to fungus, lipid transport;C:endomembrane system;PBOVMFA O.I. C.G. H.G.
9.7 99.1 62.4 At5g15850 831442 COL1 (constans-like 1) Homologous to the flowering-time gene CONSTANS. O.I. C.G. H.G.
9.6 99.1 35.6 At3g06530 819831 binding F:binding;P:unknown;C:chloroplast, vacuole;MFOPB O.I. C.G. H.G.
9.6 99.1 29.7 At2g18900 816406 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:unknown;BFMOPA O.I. C.G. H.G.
9.5 99.1 243.8 At4g30650 829188 hydrophobic protein, putative / low temperature and salt responsive protein, putative F:unknown;P:response to salt stress, hyperosmotic salinity response, response to cold;C:endomembrane system, integral to membrane;BFPMO O.I. C.G. H.G.
9.5 99.1 40.7 At2g47990 819411 SWA1 (SLOW WALKER1) Encodes a transducin family nucleolar protein with six WD40 repeats that is most likely involved in 18S rRNA biogenesis. The slow progression of the gametophytic division cycles in swa1 suggested that the SWA1 protein is required for the normal progression of mitotic division cycles through the regulation of cell metabolism. Ubiquitously expressed throughout the plant. O.I. C.G. H.G.
9.4 99.1 96.8 At1g47710 841182 serpin, putative / serine protease inhibitor, putative F:serine-type endopeptidase inhibitor activity, cysteine-type endopeptidase inhibitor activity;P:biological_process unknown;C:apoplast;MVPBOAF O.I. C.G. H.G.
9.3 99.1 22.0 At1g14580 838020 zinc finger (C2H2 type) family protein F:transcription factor activity, zinc ion binding, nucleic acid binding;P:unknown;C:intracellular;MOPFB O.I. C.G. H.G.
9.2 99.1 202.4 At3g22840 821855 ELIP1 (EARLY LIGHT-INDUCABLE PROTEIN) Encodes an early light-inducible protein. O.I. C.G. H.G.
9.2 99.1 117.9 At1g69870 843323 proton-dependent oligopeptide transport (POT) family protein F:transporter activity;P:response to salt stress, oligopeptide transport;C:plasma membrane, membrane;PBMFO O.I. C.G. H.G.
9.0 99.1 568.2 At1g20450 838633 ERD10 (EARLY RESPONSIVE TO DEHYDRATION 10) Encodes a gene induced by low temperature and dehydration. Inhibits e.coli growth while overexpressed. Belongs to the dehydrin protein family, which contains highly conserved stretches of 7-17 residues that are repetitively scattered in their sequences, the K-, S-, Y- and lysine rich segments. LTI29 and LTI30 double overexpressors confer cold tolerance. Localized to membranes and cytoplasm. O.I. C.G. H.G.
8.9 99.0 32.7 At3g55510 824716 RBL (REBELOTE) F:unknown;P:floral meristem determinacy;C:nucleus;MFOP O.I. C.G. H.G.
8.8 99.0 28.7 At3g01820 821071 adenylate kinase family protein F:nucleobase, nucleoside, nucleotide kinase activity, nucleotide kinase activity, ATP binding;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process, anaerobic respiration, nucleotide metabolic process;C:mitochondrion;BOMFPA O.I. C.G. H.G.
8.7 99.0 6.5 At5g17030 831566 UGT78D3 (UDP-GLUCOSYL TRANSFERASE 78D3) F:quercetin 3-O-glucosyltransferase activity, flavonol 3-O-arabinosyltransferase activity, UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:unknown;PMBVOF O.I. C.G. H.G.
8.6 99.0** 187.1 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.

Std2 GX	%ile	Std GX	Gene ID	Repr. ID	Gene name	Functional description	O.I.	C.G.	H.G.
105.6	99.9	230.2	At1g09350	837457	AtGolS3 (Arabidopsis thaliana galactinol synthase 3)	F:transferase activity, transferring hexosyl groups, transferase activity, transferring glycosyl groups;P:carbohydrate biosynthetic process;C:cellular_component unknown;PMFVBO	O.I.	C.G.	H.G.
39.2	99.8	469.1	At4g17090	827419	CT-BMY (CHLOROPLAST BETA-AMYLASE)	Encodes a beta-amylase targeted to the chloroplast. Transgenic BMY8 RNAi lines fail to accumulate maltose during cold shock suggesting that maltose accumulation coincides with BMY8 expression. Apart from maltose, the sugar content of the RNAi lines were similar to wildtype (glucose and sucrose unaffected).	O.I.	C.G.	H.G.
38.1	99.8	27.0	At3g55580	824723	regulator of chromosome condensation (RCC1) family protein	F:binding;P:biological_process unknown;C:cellular_component unknown;MOBPFAV	O.I.	C.G.	H.G.
27.8	99.7	26.7	At2g22590	816790	transferase, transferring glycosyl groups	F:transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBFOV	O.I.	C.G.	H.G.
23.8	99.6	489.0	At3g50970	824261	LTI30 (LOW TEMPERATURE-INDUCED 30)	Belongs to the dehydrin protein family, which contains highly conserved stretches of 7-17 residues that are repetitively scattered in their sequences, the K-, S-, Y- and lysine rich segments. LTI29 and LTI30 double overexpressors confer freeze tolerance. Located in membranes. mRNA upregulated by water deprivation and abscisic acid.	O.I.	C.G.	H.G.
23.8	99.6	68.6	At2g35960	818169	NHL12	Encodes a protein whose sequence is similar to tobacco hairpin-induced gene (HIN1) and Arabidopsis non-race specific disease resistance gene (NDR1). Expression is not altered in response to cucumber mosaic virus or spermine.	O.I.	C.G.	H.G.
22.9	99.6	66.3	At4g03400	827938	DFL2 (DWARF IN LIGHT 2)	Encodes a GH3-related gene involved in red light-specific hypocotyl elongation. Analysis of sense and antisense transgenic plants suggests that DFL2 is located downstream of red light signal transduction and determines the degree of hypocotyl elongation.	O.I.	C.G.	H.G.
22.6	99.6	105.9	At4g27560	828865	glycosyltransferase family protein	F:transferase activity, transferring glycosyl groups;P:response to salt stress, N-terminal protein myristoylation;C:cellular_component unknown;PMBFOV	O.I.	C.G.	H.G.
22.3	99.6	116.7	At5g57110	835815	ACA8 (AUTOINHIBITED CA2+ -ATPASE, ISOFORM 8)	Arabidopsis-autoinhibited Ca2+ -ATPase, isoform 8, contains all of the characteristic motifs of Ca2+ -transporting P-type Ca2+ -ATPases and is localized to the plasma membrane.	O.I.	C.G.	H.G.
22.2	99.6	60.1	At4g17550	827470	transporter-related	F:sugar:hydrogen symporter activity;P:carbohydrate transport;C:plasma membrane;BMFOPA	O.I.	C.G.	H.G.
22.1	99.6	403.7	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.
19.3	99.6	54.4	At4g34740	829626	ATASE2 (GLN PHOSPHORIBOSYL PYROPHOSPHATE AMIDOTRANSFERASE 2)	Encodes glutamine 5-phosphoribosylpyrophosphate amidotransferase. Mutants are deficient in leaf, but not cotyledon, plastid and palisade cell development. Mutants exhibit defective chloroplast development under non-low light, suggesting that the defect in chloroplast development is caused by photo-oxidative damage.	O.I.	C.G.	H.G.
18.8	99.5	43.1	At3g14890	820718	phosphoesterase	F:DNA binding, catalytic activity, zinc ion binding;P:unknown;C:unknown;MOFPVBA	O.I.	C.G.	H.G.
18.7	99.5	70.8	At5g24470	832518	APRR5 (ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5)	Encodes a pseudo-response regulator whose mutation affects various circadian-associated biological events such as flowering time in the long-day photoperiod conditions, red light sensitivity of seedlings during early photomorphogenesis, and the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light.	O.I.	C.G.	H.G.
18.6	99.5	82.4	At1g16850	838256	unknown protein	F:molecular_function unknown;P:response to salt stress;C:endomembrane system;P	O.I.	C.G.	H.G.
17.2	99.5	168.6	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.
16.4	99.5	264.4	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.
16.1	99.5	240.2	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.
15.8	99.5	98.6	At5g62210	836342	embryo-specific protein-related	F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;MPOFVBA	O.I.	C.G.	H.G.
15.7	99.5	46.7	At2g28550	817403	RAP2.7 (RELATED TO AP2.7)	F:transcription factor activity, DNA binding;P:organ morphogenesis, regulation of transcription, DNA-dependent, vegetative to reproductive phase transition;C:nucleus;POBV	O.I.	C.G.	H.G.
15.2	99.4	48.3	At1g53035	841737	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
15.1	99.4	197.4	At3g54400	824606	aspartyl protease family protein	F:aspartic-type endopeptidase activity;P:proteolysis;C:apoplast, cell wall, chloroplast, plant-type cell wall;PMFO	O.I.	C.G.	H.G.
15.1	99.4	54.0	At4g18390	827568	TCP family transcription factor, putative	F:transcription factor activity;P:regulation of transcription;C:cellular_component unknown;POMFB	O.I.	C.G.	H.G.
15.0	99.4	287.9	At2g31360	817694	ADS2 (16:0Delta9 Arabidopsis desaturase 2)	homologous to delta 9 acyl-lipid desaturases of cyanobacteria and acyl-CoA desaturases of yeast and mammals. expression up-regulated by cold temperature.	O.I.	C.G.	H.G.
15.0	99.4	27.2	At5g48070	834859	XTH20 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 20)	putative xyloglucan endotransglycosylase/hydrolase, expressed primarily in the stele of mature non-elongating regions of both the main and the lateral root. Is expressed in lateral root primordia but expression ceases after lateral root begins to grow.	O.I.	C.G.	H.G.
14.7	99.4	96.3	At3g55120	824678	TT5 (TRANSPARENT TESTA 5)	Catalyzes the conversion of chalcones into flavanones. Required for the accumulation of purple anthocyanins in leaves and stems.	O.I.	C.G.	H.G.
14.7	99.4	49.1	At2g21320	816671	zinc finger (B-box type) family protein	F:transcription factor activity, zinc ion binding;P:regulation of transcription;C:endomembrane system, intracellular;POM	O.I.	C.G.	H.G.
14.4	99.4	16.3	At1g01420	837503	UGT72B3 (UDP-GLUCOSYL TRANSFERASE 72B3)	F:quercetin 3-O-glucosyltransferase activity, UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBVOF	O.I.	C.G.	H.G.
13.5	99.4	45.4	At1g78070	844142	-	F:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;PFO	O.I.	C.G.	H.G.
12.8	99.3	68.1	At5g42570	834264	-	F:molecular_function unknown;P:intracellular protein transport;C:endoplasmic reticulum, plasma membrane;MPOFAB	O.I.	C.G.	H.G.
12.6	99.3	121.1	At1g80130	844353	binding	F:binding;P:response to oxidative stress;C:membrane;BPOMFAV	O.I.	C.G.	H.G.
12.6	99.3	28.6	At4g38400	829997	ATEXLA2 (ARABIDOPSIS THALIANA EXPANSIN-LIKE A2)	member of EXPANSIN-LIKE. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio)	O.I.	C.G.	H.G.
12.3	99.3	112.1	At1g62570	842554	FMO GS-OX4 (FLAVIN-MONOOXYGENASE GLUCOSINOLATE S-OXYGENASE 4)	belongs to the flavin-monooxygenase (FMO) family, encodes a glucosinolate S-oxygenase that catalyzes the conversion of methylthioalkyl glucosinolates to methylsulfinylalkyl glucosinolates	O.I.	C.G.	H.G.
12.2	99.3	17.8	At4g37320	829887	CYP81D5	member of CYP81D	O.I.	C.G.	H.G.
12.1	99.3	227.2	At4g27520	828861	plastocyanin-like domain-containing protein	F:electron carrier activity, copper ion binding;P:unknown;C:in 6 components;MOFBPVA	O.I.	C.G.	H.G.
12.1	99.3	32.5	At3g17130	820970	invertase/pectin methylesterase inhibitor family protein	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
12.0	99.3	408.0	At2g42540	818854	COR15A (COLD-REGULATED 15A)	A cold-regulated gene whose product is targeted to the chloroplast and constitutive expression increases freezing tolerance in protoplasts in vitro and chloroplasts in vivo. NMR and x-ray diffraction studies suggest that COR15a alters the intrinsic curvature of the inner membrane of chloroplast envelope.	O.I.	C.G.	H.G.
11.9	99.3	39.9	At1g51610	841586	cation efflux family protein / metal tolerance protein, putative (MTPc4)	F:cation transmembrane transporter activity, efflux transmembrane transporter activity;P:cation transport;C:membrane;BOMAP	O.I.	C.G.	H.G.
11.8	99.3	327.4	At2g28900	817439	ATOEP16-1 (OUTER PLASTID ENVELOPE PROTEIN 16-1)	Encodes AtOEP16, a 16-KDa plastid outer membrane protein involved in plastid import of protochlorophyllide oxidoreductase A. Predominantly expressed in leaves and is also inducible by cold treatment.	O.I.	C.G.	H.G.
11.7	99.3	131.1	At4g24960	828598	ATHVA22D	Homologous to a eukaryote specific ABA- and stress-inducible gene first isolated from barley. Groups in one subfamily with ATHVA22E. Along with other members of the ATHVA22 family, it may be involved in regulation of autophagy during development.	O.I.	C.G.	H.G.
11.4	99.3	26.9	At3g09540	820111	pectate lyase family protein	F:lyase activity, pectate lyase activity;P:N-terminal protein myristoylation;C:unknown;BPFO	O.I.	C.G.	H.G.
11.3	99.3	51.7	At1g64890	842797	integral membrane transporter family protein	F:transporter activity;P:transport;C:membrane;BOPMAF	O.I.	C.G.	H.G.
11.2	99.2	37.2	At2g24050	816939	MIF4G domain-containing protein / MA3 domain-containing protein	F:protein binding, RNA binding, binding;P:translation, RNA metabolic process;C:unknown;MPOFBV	O.I.	C.G.	H.G.
11.0	99.2	47.8	At4g32190	829352	centromeric protein-related	F:unknown;P:unknown;C:unknown;MOBFPAV	O.I.	C.G.	H.G.
10.9	99.2	20.5	At3g21540	821708	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:rRNA processing;C:nucleolus, heterotrimeric G-protein complex;MFOPBA	O.I.	C.G.	H.G.
10.7	99.2	78.1	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.
10.7	99.2	77.7	At2g31380	817696	STH	a B-box zinc finger protein that interacts with COP1. contains a novel 11 amino acid motif at the C-terminus (also found at the N-terminus of HY5) that is involved in the COP1 interaction.	O.I.	C.G.	H.G.
10.6	99.2	22.0	At5g47650	834816	ATNUDT2 (ARABIDOPSIS THALIANA NUDIX HYDROLASE HOMOLOG 2)	Encodes an ADP-ribose pyrophosphatase that confers enhanced tolerance to oxidative stress.	O.I.	C.G.	H.G.
10.5	99.2	47.4	At1g27760	839669	interferon-related developmental regulator family protein / IFRD protein family	Encodes a protein with similarity to human interferon-related developmental regulator (IFRD)that is involved in salt tolerance. Loss of function mutations are hypersensitive to salt stress and have reduced fertility. SAT32 is found in the cytoplasm but appears to translocate to the nucleus when plants are subject to salt stress.	O.I.	C.G.	H.G.
10.4	99.2	37.3	At1g49720	841395	ABF1 (ABSCISIC ACID RESPONSIVE ELEMENT-BINDING FACTOR 1)	Identified as a protein that binds to abscisic acid response elements. May mediate transcriptional regulation of ABA responses.	O.I.	C.G.	H.G.
10.4	99.2	35.8	At3g10530	820218	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;BMFOPA	O.I.	C.G.	H.G.
10.3	99.2	538.0	At1g20440	838632	COR47 (COLD-REGULATED 47)	Belongs to the dehydrin protein family, which contains highly conserved stretches of 7-17 residues that are repetitively scattered in their sequences, the K-, S-, Y- and lysine rich segments. Cold regulated gene, amino acid sequence homology with Group II LEA (late embryogenesis abundant) proteins. Also responds to osmotic stress, ABA, dehydration and inhibits e.coli growth while overexpressed. COR47 and RAB18 double overexpressor plants are cold tolerant.	O.I.	C.G.	H.G.
10.3	99.2	27.4	At1g03530	839468	NAF1 (NUCLEAR ASSEMBLY FACTOR 1)	F:unknown;P:biological_process unknown;C:unknown;MOBFPVA	O.I.	C.G.	H.G.
10.2	99.2	33.6	At1g71710	843501	inositol polyphosphate 5-phosphatase, putative	F:inositol-polyphosphate 5-phosphatase activity, inositol or phosphatidylinositol phosphatase activity;P:biological_process unknown;C:cellular_component unknown;MFPOV	O.I.	C.G.	H.G.
10.0	99.2	38.3	At1g24530	839068	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:plasma membrane, heterotrimeric G-protein complex;MFOBPA	O.I.	C.G.	H.G.
10.0	99.2	12.1	At3g62690	825443	ATL5 (ATL5)	Encodes a RING-H2 zinc finger protein related to ATL2. The ATL gene family is represented by fifteen sequences that contain, in addition to the RING, a transmembrane domain which is located in most of them towards the N-terminal end.	O.I.	C.G.	H.G.
9.8	99.1	23.0	At4g04940	825833	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:rRNA processing;C:CUL4 RING ubiquitin ligase complex;MFBOPA	O.I.	C.G.	H.G.
9.7	99.1	363.7	At4g12470	826859	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	F:lipid binding;P:defense response to fungus, lipid transport;C:endomembrane system;PBOVMFA	O.I.	C.G.	H.G.
9.7	99.1	62.4	At5g15850	831442	COL1 (constans-like 1)	Homologous to the flowering-time gene CONSTANS.	O.I.	C.G.	H.G.
9.6	99.1	35.6	At3g06530	819831	binding	F:binding;P:unknown;C:chloroplast, vacuole;MFOPB	O.I.	C.G.	H.G.
9.6	99.1	29.7	At2g18900	816406	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:unknown;BFMOPA	O.I.	C.G.	H.G.
9.5	99.1	243.8	At4g30650	829188	hydrophobic protein, putative / low temperature and salt responsive protein, putative	F:unknown;P:response to salt stress, hyperosmotic salinity response, response to cold;C:endomembrane system, integral to membrane;BFPMO	O.I.	C.G.	H.G.
9.5	99.1	40.7	At2g47990	819411	SWA1 (SLOW WALKER1)	Encodes a transducin family nucleolar protein with six WD40 repeats that is most likely involved in 18S rRNA biogenesis. The slow progression of the gametophytic division cycles in swa1 suggested that the SWA1 protein is required for the normal progression of mitotic division cycles through the regulation of cell metabolism. Ubiquitously expressed throughout the plant.	O.I.	C.G.	H.G.
9.4	99.1	96.8	At1g47710	841182	serpin, putative / serine protease inhibitor, putative	F:serine-type endopeptidase inhibitor activity, cysteine-type endopeptidase inhibitor activity;P:biological_process unknown;C:apoplast;MVPBOAF	O.I.	C.G.	H.G.
9.3	99.1	22.0	At1g14580	838020	zinc finger (C2H2 type) family protein	F:transcription factor activity, zinc ion binding, nucleic acid binding;P:unknown;C:intracellular;MOPFB	O.I.	C.G.	H.G.
9.2	99.1	202.4	At3g22840	821855	ELIP1 (EARLY LIGHT-INDUCABLE PROTEIN)	Encodes an early light-inducible protein.	O.I.	C.G.	H.G.
9.2	99.1	117.9	At1g69870	843323	proton-dependent oligopeptide transport (POT) family protein	F:transporter activity;P:response to salt stress, oligopeptide transport;C:plasma membrane, membrane;PBMFO	O.I.	C.G.	H.G.
9.0	99.1	568.2	At1g20450	838633	ERD10 (EARLY RESPONSIVE TO DEHYDRATION 10)	Encodes a gene induced by low temperature and dehydration. Inhibits e.coli growth while overexpressed. Belongs to the dehydrin protein family, which contains highly conserved stretches of 7-17 residues that are repetitively scattered in their sequences, the K-, S-, Y- and lysine rich segments. LTI29 and LTI30 double overexpressors confer cold tolerance. Localized to membranes and cytoplasm.	O.I.	C.G.	H.G.
8.9	99.0	32.7	At3g55510	824716	RBL (REBELOTE)	F:unknown;P:floral meristem determinacy;C:nucleus;MFOP	O.I.	C.G.	H.G.
8.8	99.0	28.7	At3g01820	821071	adenylate kinase family protein	F:nucleobase, nucleoside, nucleotide kinase activity, nucleotide kinase activity, ATP binding;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process, anaerobic respiration, nucleotide metabolic process;C:mitochondrion;BOMFPA	O.I.	C.G.	H.G.
8.7	99.0	6.5	At5g17030	831566	UGT78D3 (UDP-GLUCOSYL TRANSFERASE 78D3)	F:quercetin 3-O-glucosyltransferase activity, flavonol 3-O-arabinosyltransferase activity, UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:unknown;PMBVOF	O.I.	C.G.	H.G.
8.6	99.0	187.1	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.

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GSM ID	GSM128793
Assay name	Zarka_1-5_MT-WT24HA_Rep1_ATH1
GSE experiment	GSE5534: Response to cold, plate grown plants

Microarray experiments to specifically-expressed genes

GSM ID GSM128793 Assay name Zarka_1-5_MT-WT24HA_Rep1_ATH1 GSE experiment GSE5534: Response to cold, plate grown plants

GSM ID GSM128793

Assay name Zarka_1-5_MT-WT24HA_Rep1_ATH1

GSE experiment GSE5534: Response to cold, plate grown plants