CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM128657

Assay name Underwood_1-10_Mock-Inoculum-24h_Rep1_ATH1

GSE experiment GSE5520: Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction

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
29.6 99.7 38.2 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.
24.2 99.6 36.2 At2g42040 818804 - F:molecular_function unknown;P:biological_process unknown;C:unknown;PMO O.I. C.G. H.G.
23.6 99.6 58.6 At1g18620 838443 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBV O.I. C.G. H.G.
20.7 99.6 124.0 At3g54500 824615 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB O.I. C.G. H.G.
20.4 99.6 74.0 At3g13062 820493 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO O.I. C.G. H.G.
19.5 99.6 16.6 At1g75250 843862 ATRL6 (ARABIDOPSIS RAD-LIKE 6) F:transcription factor activity;P:regulation of transcription;C:unknown;PMO O.I. C.G. H.G.
18.9 99.5 29.9 At3g50750 824239 brassinosteroid signalling positive regulator-related F:transcription regulator activity;P:biological_process unknown;C:vacuole;OPFMB O.I. C.G. H.G.
18.7 99.5 16.2 At1g29460 839822 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:mitochondrion;P O.I. C.G. H.G.
18.2 99.5 39.8 At3g58120 824981 BZIP61 Encodes a member of the BZIP family of transcription factors. Forms heterodimers with the related protein AtbZIP34. Binds to G-boxes in vitro and is localized to the nucleus in onion epidermal cells. O.I. C.G. H.G.
18.0 99.5 54.4 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.
17.3 99.5 291.9 At3g13750 820584 BGAL1 (Beta galactosidase 1) beta-galactosidase, glycosyl hydrolase family 35 O.I. C.G. H.G.
17.2 99.5 50.9 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.
17.1 99.5 19.5 At4g38850 830040 SAUR15 (SMALL AUXIN UPREGULATED 15) mRNA is rapidly induced by auxin and is very short-lived. Has been used as a reporter gene in studying auxin mutants. O.I. C.G. H.G.
16.9 99.5 151.4 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.
16.9 99.5 81.3 At1g14280 837989 PKS2 (PHYTOCHROME KINASE SUBSTRATE 2) Encodes phytochrome kinase substrate 2. PKS proteins are critical for hypocotyl phototropism. O.I. C.G. H.G.
16.8 99.5 84.1 At2g18300 816346 basic helix-loop-helix (bHLH) family protein F:transcription factor activity;P:response to cytokinin stimulus, regulation of transcription;C:nucleus;PMFO O.I. C.G. H.G.
16.4 99.5 163.3 At5g16030 831460 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPVBA O.I. C.G. H.G.
16.4 99.5 35.1 At3g19850 821522 phototropic-responsive NPH3 family protein F:protein binding, signal transducer activity;P:response to light stimulus;C:endomembrane system;P O.I. C.G. H.G.
16.1 99.5 8.3 At5g04190 830297 PKS4 (phytochrome kinase substrate 4) Encodes phytochrome kinase substrate 4, a phytochrome signaling component involved in phototropism. O.I. C.G. H.G.
15.7 99.5 96.2 At1g14920 838057 GAI (GIBBERELLIC ACID INSENSITIVE) Similar to a putative transcription factor and transcriptional coactivators. Repressor of GA responses and involved in gibberellic acid mediated signaling. Member of the DELLA proteins that restrain the cell proliferation and expansion that drives plant growth. The protein undergoes degradation in response to GA via the 26S proteasome. GAI may be involved in reducing ROS accumulation in response to stress by up-regulating the transcription of superoxide dismutases. Represses GA-induced vegetative growth and floral initiation. Rapidly degraded in response to GA. O.I. C.G. H.G.
15.6 99.5 61.9 At5g28020 832872 CYSD2 (CYSTEINE SYNTHASE D2) Encodes cysteine synthase CysD2. O.I. C.G. H.G.
15.4 99.5 96.9 At5g02760 831234 protein phosphatase 2C family protein / PP2C family protein F:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:protein serine/threonine phosphatase complex;PMOFBAV O.I. C.G. H.G.
15.0 99.4 36.0 At1g73830 843719 BEE3 (BR ENHANCED EXPRESSION 3) F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PFMBO O.I. C.G. H.G.
14.7 99.4 107.6 At2g30600 817610 BTB/POZ domain-containing protein F:protein binding;P:cell adhesion;C:cellular_component unknown;MPOVF O.I. C.G. H.G.
13.8 99.4 59.5 At5g18630 831981 lipase class 3 family protein F:triacylglycerol lipase activity;P:lipid metabolic process;C:endomembrane system;PFOBMV O.I. C.G. H.G.
13.5 99.4 5.3 At2g42380 818839 bZIP transcription factor family protein Encodes a member of the BZIP family of transcription factors. Forms heterodimers with the related protein AtbZIP61. Binds to G-boxes in vitro and is localized to the nucleus in onion epidermal cells. O.I. C.G. H.G.
13.4 99.4 46.1 At4g01330 828117 ATP binding / kinase/ protein kinase/ protein serine/threonine kinase/ protein tyrosine kinase F:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA O.I. C.G. H.G.
12.9 99.3 42.4 At4g16990 827407 RLM3 (RESISTANCE TO LEPTOSPHAERIA MACULANS 3) F:transmembrane receptor activity, ATP binding;P:defense response to fungus, incompatible interaction, jasmonic acid and ethylene-dependent systemic resistance, callose deposition during defense response, defense response;C:intrinsic to membrane;PMB O.I. C.G. H.G.
12.8 99.3 62.5 At5g12050 831078 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFB O.I. C.G. H.G.
12.4 99.3 113.3 At1g63800 842683 UBC5 (ubiquitin-conjugating enzyme 5) F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;MFOPV O.I. C.G. H.G.
12.3 99.3 139.5 At1g52190 841649 proton-dependent oligopeptide transport (POT) family protein F:transporter activity;P:oligopeptide transport;C:membrane;PBMFO O.I. C.G. H.G.
12.1 99.3 136.7 At1g80180 844358 unknown protein F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;P O.I. C.G. H.G.
11.9 99.3 393.0 At3g16770 820929 ATEBP (ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN) Encodes a member of the ERF (ethylene response factor) subfamily B-2 of the plant specific ERF/AP2 transcription factor family (RAP2.3). The protein contains one AP2 domain. There are 5 members in this subfamily including RAP2.2 AND RAP2.12.It is localized to the nucleus and acts as a transcriptional activator through the GCC-box. It has been identified as a suppressor of Bax-induced cell death by functional screening in yeast and can also suppress Bax-induced cell death in tobacco plants. Overexpression of this gene in tobacco BY-2 cells confers resistance to H2O2 and heat stresses. Overexpression in Arabidopsis causes upregulation of PDF1.2 and GST6. It is part of the ethylene signaling pathway and is predicted to act downstream of EIN2 and CTR1, but not under EIN3. O.I. C.G. H.G.
11.9 99.3 25.8 At5g52900 835367 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
11.7 99.3 97.6 At4g19420 827683 pectinacetylesterase family protein F:carboxylesterase activity;P:biological_process unknown;C:endomembrane system;PMOBA O.I. C.G. H.G.
11.7 99.3 33.7 At5g60860 836207 AtRABA1f (Arabidopsis Rab GTPase homolog A1f) F:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:unknown;MOFPBAV O.I. C.G. H.G.
11.6 99.3 113.9 At5g57655 835871 xylose isomerase family protein F:xylose isomerase activity;P:carbohydrate metabolic process;C:endoplasmic reticulum, plasma membrane, vacuole;BOPMF O.I. C.G. H.G.
11.6 99.3 45.1 At4g08470 826406 MAPKKK10 member of MEKK subfamily O.I. C.G. H.G.
11.5 99.3 36.8 At3g03870 821099 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM O.I. C.G. H.G.
11.5 99.3 31.3 At5g43270 834345 SPL2 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2) member of the SPL (squamosa-promoter binding protein-like) gene family, a novel gene family encoding DNA binding proteins and putative transcription factors. The genes are characterized by the presence of the SBP-box, which encodes a protein domain, the O.I. C.G. H.G.
11.5 99.3 26.1 At5g44260 834449 zinc finger (CCCH-type) family protein F:transcription factor activity, nucleic acid binding;P:unknown;C:unknown;MOPFV O.I. C.G. H.G.
11.4 99.3 36.9 At1g10020 837537 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFMO O.I. C.G. H.G.
11.4 99.3 11.9 At3g29670 822645 transferase family protein F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFO O.I. C.G. H.G.
11.3 99.3 39.3 At2g18290 816345 anaphase-promoting complex, subunit 10 family / APC10 family F:protein binding;P:regulation of mitotic metaphase/anaphase transition;C:anaphase-promoting complex;MFOP O.I. C.G. H.G.
11.2 99.2 48.6 At4g38860 830041 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. C.G. H.G.
11.0 99.2 49.7 At3g26280 822231 CYP71B4 cytochrome P450 monooxygenase O.I. C.G. H.G.
10.9 99.2 226.7 At1g74670 843806 gibberellin-responsive protein, putative F:molecular_function unknown;P:response to fructose stimulus, response to gibberellin stimulus, response to sucrose stimulus, gibberellic acid mediated signaling, response to glucose stimulus;C:endomembrane system;P O.I. C.G. H.G.
10.9 99.2 125.6 At5g02840 831766 LCL1 (LHY/CCA1-like 1) 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.
10.9 99.2 34.4 At2g35060 818071 KUP11 potassium transporter O.I. C.G. H.G.
10.6 99.2 53.1 At4g30993 829225 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
10.5 99.2 58.1 At3g07010 819886 pectate lyase family protein F:lyase activity, pectate lyase activity;P:biological_process unknown;C:endomembrane system;PBFO O.I. C.G. H.G.
10.4 99.2 41.9 At5g59080 836025 unknown protein F:molecular_function unknown;P:response to oxidative stress;C:chloroplast;P O.I. C.G. H.G.
10.4 99.2 10.0 At1g19510 838537 ATRL5 (ARABIDOPSIS RAD-LIKE 5) F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:unknown;PMO O.I. C.G. H.G.
10.3 99.2 143.2 At5g40450 834043 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast, plasma membrane;MOBFPAV O.I. C.G. H.G.
10.3 99.2 32.5 At3g61210 825293 embryo-abundant protein-related F:unknown;P:unknown;C:cellular_component unknown;BPFOMA O.I. C.G. H.G.
10.2 99.2 57.4 At2g04690 815012 cellular repressor of E1A-stimulated genes (CREG) family F:FMN binding;P:biological_process unknown;C:vacuole;MBOPF O.I. C.G. H.G.
10.1 99.2 12.1 At2g46250 819233 myosin heavy chain-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAV O.I. C.G. H.G.
10.0 99.2 66.8 At3g16850 820938 glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein F:polygalacturonase activity;P:carbohydrate metabolic process;C:vacuole, plant-type cell wall;PBFOMA O.I. C.G. H.G.
10.0 99.2 28.1 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.
9.7 99.1 49.6 At3g57410 824908 VLN3 (VILLIN 3) Encodes a protein with high homology to animal villin. O.I. C.G. H.G.
9.7 99.1 19.9 At3g26220 822223 CYP71B3 cytochrome P450 monooxygenase O.I. C.G. H.G.
9.7 99.1 13.9 At1g78270 844162 AtUGT85A4 (UDP-glucosyl transferase 85A4) F:transferase activity, transferring hexosyl groups, UDP-glycosyltransferase activity, glucuronosyltransferase activity;P:metabolic process;C:cellular_component unknown;PMVBFO O.I. C.G. H.G.
9.6 99.1 21.3 At2g23130 816845 AGP17 (ARABINOGALACTAN PROTEIN 17) AGP17 is a lysine-rich arabinogalactan-protein (AGP) and part of a multi-gene family of glycoproteins with approx. 50 members. It falls into one subclass with AGP18 and AGP19, other lysine-rich AGPs. 84% of its proline residues are hydroxylated to hydroproline and its heavy glycosylation accounts for appr. 69% of the molecular weight. The main glycosyl residues are arabinose (30.1%) and galactose (55.1%). Glycosyl linkages are consistent with type II arabinogalactans. AGP17 is predicted to have a glycosylphosphatidylinositol (GPI)anchor and is localized to the plasma membrane and Hechtian strands. It is expressed in young/old leaves, shoots, suspension cultures and flowers. O.I. C.G. H.G.
9.5 99.1 168.5 At2g39570 818542 ACT domain-containing protein F:amino acid binding;P:metabolic process;C:unknown;POB O.I. C.G. H.G.
9.5 99.1 85.6 At1g58180 842185 carbonic anhydrase family protein / carbonate dehydratase family protein F:carbonate dehydratase activity, zinc ion binding;P:carbon utilization;C:mitochondrion;BOPFMA O.I. C.G. H.G.
9.5 99.1 51.4 At5g28770 832990 BZO2H3 bZIP protein BZO2H3 mRNA, partial cds O.I. C.G. H.G.
9.2 99.1 33.1 At5g18060 831310 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. C.G. H.G.
8.9 99.0 37.7 At5g62280 836349 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
8.9 99.0 22.7 At2g45530 819161 zinc finger (C3HC4-type RING finger) family protein F:zinc ion binding;P:unknown;C:unknown;PMOFV O.I. C.G. H.G.
8.8 99.0 242.0 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.
8.8 99.0 115.4 At3g45780 823721 PHOT1 (PHOTOTROPIN 1) Blue-light photoreceptor. Contains a light activated serine-threonine kinase domain and LOV1 and LOV2 repeats. Mutants are defective in blue-light response. Mediates blue light-induced growth enhancements. PHOT1 and PHOT2 mediate blue light-dependent activation of the plasma membrane H+-ATPase in guard cell protoplasts. PHOT1 undergoes blue-light-dependent autophosphorylation. At least eight phosphorylation sites have been identified in PHOT1. Phosphorylation of serine851 in the activation loop of PHOT1 appears to be required for stomatal opening, chloroplast accumulation, leaf flattening, and phototropism, and phosphorylation of serine849 may also contribute to the regulation of these responses. Phosphorylation-dependent binding of 14-3-3 proteins to the Hinge1 region of PHOT1 appears to require serine350 and serine376. O.I. C.G. H.G.
8.8 99.0 42.7 At4g08920 826470 CRY1 (CRYPTOCHROME 1) Encodes CRY1, a flavin-type blue-light photoreceptor with ATP binding and autophosphorylation activity. The photoreceptor may be involved in electron transport. Mutant phenotype displays a blue light-dependent inhibition of hypocotyl elongation. Photoreceptor activity requires light-induced homodimerisation of the N-terminal CNT1 domains of CRY1. Involved in blue-light induced stomatal opening. The C-terminal domain of the protein undergoes a light dependent conformational change. Also involved in response to circadian rhythm. Mutants exhibit long hypocotyl under blue light and are out of phase in their response to circadian rhythm. CRY1 is present in the nucleus and cytoplasm. Different subcellular pools of CRY1 have different functions during photomorphogenesis of Arabidopsis seedlings. O.I. C.G. H.G.
8.7 99.0 246.8 At1g11260 837667 STP1 (SUGAR TRANSPORTER 1) Encodes a H+/hexose cotransporter. O.I. C.G. H.G.
8.6 99.0 263.2 At5g49360 834996 BXL1 (BETA-XYLOSIDASE 1) Encodes a bifunctional {beta}-D-xylosidase/{alpha}-L-arabinofuranosidase required for pectic arabinan modification. Located in the extracellular matrix. Gene is expressed specifically in tissues undergoing secondary wall thickening. This is a member of glycosyl hydrolase family 3 and has six other closely related members. O.I. C.G. H.G.
8.6 99.0 84.9 At5g63800 836500 MUM2 (MUCILAGE-MODIFIED 2) Involved in mucilage formation. Mutants form columella and outer cell wall architecture of the mucilage cells resembles wild-type. However, mum2 seeds completely lack seed coat mucilage. This mutation appears to represent a later step in the development of this cell-type. Encodes a beta-galactosidase involved in seed coat mucilage biosynthesis. Member of Glycoside Hydrolase Family 35 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.
29.6	99.7	38.2	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.
24.2	99.6	36.2	At2g42040	818804	-	F:molecular_function unknown;P:biological_process unknown;C:unknown;PMO	O.I.	C.G.	H.G.
23.6	99.6	58.6	At1g18620	838443	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBV	O.I.	C.G.	H.G.
20.7	99.6	124.0	At3g54500	824615	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB	O.I.	C.G.	H.G.
20.4	99.6	74.0	At3g13062	820493	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO	O.I.	C.G.	H.G.
19.5	99.6	16.6	At1g75250	843862	ATRL6 (ARABIDOPSIS RAD-LIKE 6)	F:transcription factor activity;P:regulation of transcription;C:unknown;PMO	O.I.	C.G.	H.G.
18.9	99.5	29.9	At3g50750	824239	brassinosteroid signalling positive regulator-related	F:transcription regulator activity;P:biological_process unknown;C:vacuole;OPFMB	O.I.	C.G.	H.G.
18.7	99.5	16.2	At1g29460	839822	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:mitochondrion;P	O.I.	C.G.	H.G.
18.2	99.5	39.8	At3g58120	824981	BZIP61	Encodes a member of the BZIP family of transcription factors. Forms heterodimers with the related protein AtbZIP34. Binds to G-boxes in vitro and is localized to the nucleus in onion epidermal cells.	O.I.	C.G.	H.G.
18.0	99.5	54.4	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.
17.3	99.5	291.9	At3g13750	820584	BGAL1 (Beta galactosidase 1)	beta-galactosidase, glycosyl hydrolase family 35	O.I.	C.G.	H.G.
17.2	99.5	50.9	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.
17.1	99.5	19.5	At4g38850	830040	SAUR15 (SMALL AUXIN UPREGULATED 15)	mRNA is rapidly induced by auxin and is very short-lived. Has been used as a reporter gene in studying auxin mutants.	O.I.	C.G.	H.G.
16.9	99.5	151.4	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.
16.9	99.5	81.3	At1g14280	837989	PKS2 (PHYTOCHROME KINASE SUBSTRATE 2)	Encodes phytochrome kinase substrate 2. PKS proteins are critical for hypocotyl phototropism.	O.I.	C.G.	H.G.
16.8	99.5	84.1	At2g18300	816346	basic helix-loop-helix (bHLH) family protein	F:transcription factor activity;P:response to cytokinin stimulus, regulation of transcription;C:nucleus;PMFO	O.I.	C.G.	H.G.
16.4	99.5	163.3	At5g16030	831460	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPVBA	O.I.	C.G.	H.G.
16.4	99.5	35.1	At3g19850	821522	phototropic-responsive NPH3 family protein	F:protein binding, signal transducer activity;P:response to light stimulus;C:endomembrane system;P	O.I.	C.G.	H.G.
16.1	99.5	8.3	At5g04190	830297	PKS4 (phytochrome kinase substrate 4)	Encodes phytochrome kinase substrate 4, a phytochrome signaling component involved in phototropism.	O.I.	C.G.	H.G.
15.7	99.5	96.2	At1g14920	838057	GAI (GIBBERELLIC ACID INSENSITIVE)	Similar to a putative transcription factor and transcriptional coactivators. Repressor of GA responses and involved in gibberellic acid mediated signaling. Member of the DELLA proteins that restrain the cell proliferation and expansion that drives plant growth. The protein undergoes degradation in response to GA via the 26S proteasome. GAI may be involved in reducing ROS accumulation in response to stress by up-regulating the transcription of superoxide dismutases. Represses GA-induced vegetative growth and floral initiation. Rapidly degraded in response to GA.	O.I.	C.G.	H.G.
15.6	99.5	61.9	At5g28020	832872	CYSD2 (CYSTEINE SYNTHASE D2)	Encodes cysteine synthase CysD2.	O.I.	C.G.	H.G.
15.4	99.5	96.9	At5g02760	831234	protein phosphatase 2C family protein / PP2C family protein	F:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:protein serine/threonine phosphatase complex;PMOFBAV	O.I.	C.G.	H.G.
15.0	99.4	36.0	At1g73830	843719	BEE3 (BR ENHANCED EXPRESSION 3)	F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PFMBO	O.I.	C.G.	H.G.
14.7	99.4	107.6	At2g30600	817610	BTB/POZ domain-containing protein	F:protein binding;P:cell adhesion;C:cellular_component unknown;MPOVF	O.I.	C.G.	H.G.
13.8	99.4	59.5	At5g18630	831981	lipase class 3 family protein	F:triacylglycerol lipase activity;P:lipid metabolic process;C:endomembrane system;PFOBMV	O.I.	C.G.	H.G.
13.5	99.4	5.3	At2g42380	818839	bZIP transcription factor family protein	Encodes a member of the BZIP family of transcription factors. Forms heterodimers with the related protein AtbZIP61. Binds to G-boxes in vitro and is localized to the nucleus in onion epidermal cells.	O.I.	C.G.	H.G.
13.4	99.4	46.1	At4g01330	828117	ATP binding / kinase/ protein kinase/ protein serine/threonine kinase/ protein tyrosine kinase	F:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA	O.I.	C.G.	H.G.
12.9	99.3	42.4	At4g16990	827407	RLM3 (RESISTANCE TO LEPTOSPHAERIA MACULANS 3)	F:transmembrane receptor activity, ATP binding;P:defense response to fungus, incompatible interaction, jasmonic acid and ethylene-dependent systemic resistance, callose deposition during defense response, defense response;C:intrinsic to membrane;PMB	O.I.	C.G.	H.G.
12.8	99.3	62.5	At5g12050	831078	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFB	O.I.	C.G.	H.G.
12.4	99.3	113.3	At1g63800	842683	UBC5 (ubiquitin-conjugating enzyme 5)	F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;MFOPV	O.I.	C.G.	H.G.
12.3	99.3	139.5	At1g52190	841649	proton-dependent oligopeptide transport (POT) family protein	F:transporter activity;P:oligopeptide transport;C:membrane;PBMFO	O.I.	C.G.	H.G.
12.1	99.3	136.7	At1g80180	844358	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;P	O.I.	C.G.	H.G.
11.9	99.3	393.0	At3g16770	820929	ATEBP (ETHYLENE-RESPONSIVE ELEMENT BINDING PROTEIN)	Encodes a member of the ERF (ethylene response factor) subfamily B-2 of the plant specific ERF/AP2 transcription factor family (RAP2.3). The protein contains one AP2 domain. There are 5 members in this subfamily including RAP2.2 AND RAP2.12.It is localized to the nucleus and acts as a transcriptional activator through the GCC-box. It has been identified as a suppressor of Bax-induced cell death by functional screening in yeast and can also suppress Bax-induced cell death in tobacco plants. Overexpression of this gene in tobacco BY-2 cells confers resistance to H2O2 and heat stresses. Overexpression in Arabidopsis causes upregulation of PDF1.2 and GST6. It is part of the ethylene signaling pathway and is predicted to act downstream of EIN2 and CTR1, but not under EIN3.	O.I.	C.G.	H.G.
11.9	99.3	25.8	At5g52900	835367	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
11.7	99.3	97.6	At4g19420	827683	pectinacetylesterase family protein	F:carboxylesterase activity;P:biological_process unknown;C:endomembrane system;PMOBA	O.I.	C.G.	H.G.
11.7	99.3	33.7	At5g60860	836207	AtRABA1f (Arabidopsis Rab GTPase homolog A1f)	F:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:unknown;MOFPBAV	O.I.	C.G.	H.G.
11.6	99.3	113.9	At5g57655	835871	xylose isomerase family protein	F:xylose isomerase activity;P:carbohydrate metabolic process;C:endoplasmic reticulum, plasma membrane, vacuole;BOPMF	O.I.	C.G.	H.G.
11.6	99.3	45.1	At4g08470	826406	MAPKKK10	member of MEKK subfamily	O.I.	C.G.	H.G.
11.5	99.3	36.8	At3g03870	821099	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM	O.I.	C.G.	H.G.
11.5	99.3	31.3	At5g43270	834345	SPL2 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2)	member of the SPL (squamosa-promoter binding protein-like) gene family, a novel gene family encoding DNA binding proteins and putative transcription factors. The genes are characterized by the presence of the SBP-box, which encodes a protein domain, the	O.I.	C.G.	H.G.
11.5	99.3	26.1	At5g44260	834449	zinc finger (CCCH-type) family protein	F:transcription factor activity, nucleic acid binding;P:unknown;C:unknown;MOPFV	O.I.	C.G.	H.G.
11.4	99.3	36.9	At1g10020	837537	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFMO	O.I.	C.G.	H.G.
11.4	99.3	11.9	At3g29670	822645	transferase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFO	O.I.	C.G.	H.G.
11.3	99.3	39.3	At2g18290	816345	anaphase-promoting complex, subunit 10 family / APC10 family	F:protein binding;P:regulation of mitotic metaphase/anaphase transition;C:anaphase-promoting complex;MFOP	O.I.	C.G.	H.G.
11.2	99.2	48.6	At4g38860	830041	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	C.G.	H.G.
11.0	99.2	49.7	At3g26280	822231	CYP71B4	cytochrome P450 monooxygenase	O.I.	C.G.	H.G.
10.9	99.2	226.7	At1g74670	843806	gibberellin-responsive protein, putative	F:molecular_function unknown;P:response to fructose stimulus, response to gibberellin stimulus, response to sucrose stimulus, gibberellic acid mediated signaling, response to glucose stimulus;C:endomembrane system;P	O.I.	C.G.	H.G.
10.9	99.2	125.6	At5g02840	831766	LCL1 (LHY/CCA1-like 1)	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.
10.9	99.2	34.4	At2g35060	818071	KUP11	potassium transporter	O.I.	C.G.	H.G.
10.6	99.2	53.1	At4g30993	829225	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
10.5	99.2	58.1	At3g07010	819886	pectate lyase family protein	F:lyase activity, pectate lyase activity;P:biological_process unknown;C:endomembrane system;PBFO	O.I.	C.G.	H.G.
10.4	99.2	41.9	At5g59080	836025	unknown protein	F:molecular_function unknown;P:response to oxidative stress;C:chloroplast;P	O.I.	C.G.	H.G.
10.4	99.2	10.0	At1g19510	838537	ATRL5 (ARABIDOPSIS RAD-LIKE 5)	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:unknown;PMO	O.I.	C.G.	H.G.
10.3	99.2	143.2	At5g40450	834043	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast, plasma membrane;MOBFPAV	O.I.	C.G.	H.G.
10.3	99.2	32.5	At3g61210	825293	embryo-abundant protein-related	F:unknown;P:unknown;C:cellular_component unknown;BPFOMA	O.I.	C.G.	H.G.
10.2	99.2	57.4	At2g04690	815012	cellular repressor of E1A-stimulated genes (CREG) family	F:FMN binding;P:biological_process unknown;C:vacuole;MBOPF	O.I.	C.G.	H.G.
10.1	99.2	12.1	At2g46250	819233	myosin heavy chain-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAV	O.I.	C.G.	H.G.
10.0	99.2	66.8	At3g16850	820938	glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein	F:polygalacturonase activity;P:carbohydrate metabolic process;C:vacuole, plant-type cell wall;PBFOMA	O.I.	C.G.	H.G.
10.0	99.2	28.1	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.
9.7	99.1	49.6	At3g57410	824908	VLN3 (VILLIN 3)	Encodes a protein with high homology to animal villin.	O.I.	C.G.	H.G.
9.7	99.1	19.9	At3g26220	822223	CYP71B3	cytochrome P450 monooxygenase	O.I.	C.G.	H.G.
9.7	99.1	13.9	At1g78270	844162	AtUGT85A4 (UDP-glucosyl transferase 85A4)	F:transferase activity, transferring hexosyl groups, UDP-glycosyltransferase activity, glucuronosyltransferase activity;P:metabolic process;C:cellular_component unknown;PMVBFO	O.I.	C.G.	H.G.
9.6	99.1	21.3	At2g23130	816845	AGP17 (ARABINOGALACTAN PROTEIN 17)	AGP17 is a lysine-rich arabinogalactan-protein (AGP) and part of a multi-gene family of glycoproteins with approx. 50 members. It falls into one subclass with AGP18 and AGP19, other lysine-rich AGPs. 84% of its proline residues are hydroxylated to hydroproline and its heavy glycosylation accounts for appr. 69% of the molecular weight. The main glycosyl residues are arabinose (30.1%) and galactose (55.1%). Glycosyl linkages are consistent with type II arabinogalactans. AGP17 is predicted to have a glycosylphosphatidylinositol (GPI)anchor and is localized to the plasma membrane and Hechtian strands. It is expressed in young/old leaves, shoots, suspension cultures and flowers.	O.I.	C.G.	H.G.
9.5	99.1	168.5	At2g39570	818542	ACT domain-containing protein	F:amino acid binding;P:metabolic process;C:unknown;POB	O.I.	C.G.	H.G.
9.5	99.1	85.6	At1g58180	842185	carbonic anhydrase family protein / carbonate dehydratase family protein	F:carbonate dehydratase activity, zinc ion binding;P:carbon utilization;C:mitochondrion;BOPFMA	O.I.	C.G.	H.G.
9.5	99.1	51.4	At5g28770	832990	BZO2H3	bZIP protein BZO2H3 mRNA, partial cds	O.I.	C.G.	H.G.
9.2	99.1	33.1	At5g18060	831310	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	C.G.	H.G.
8.9	99.0	37.7	At5g62280	836349	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
8.9	99.0	22.7	At2g45530	819161	zinc finger (C3HC4-type RING finger) family protein	F:zinc ion binding;P:unknown;C:unknown;PMOFV	O.I.	C.G.	H.G.
8.8	99.0	242.0	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.
8.8	99.0	115.4	At3g45780	823721	PHOT1 (PHOTOTROPIN 1)	Blue-light photoreceptor. Contains a light activated serine-threonine kinase domain and LOV1 and LOV2 repeats. Mutants are defective in blue-light response. Mediates blue light-induced growth enhancements. PHOT1 and PHOT2 mediate blue light-dependent activation of the plasma membrane H+-ATPase in guard cell protoplasts. PHOT1 undergoes blue-light-dependent autophosphorylation. At least eight phosphorylation sites have been identified in PHOT1. Phosphorylation of serine851 in the activation loop of PHOT1 appears to be required for stomatal opening, chloroplast accumulation, leaf flattening, and phototropism, and phosphorylation of serine849 may also contribute to the regulation of these responses. Phosphorylation-dependent binding of 14-3-3 proteins to the Hinge1 region of PHOT1 appears to require serine350 and serine376.	O.I.	C.G.	H.G.
8.8	99.0	42.7	At4g08920	826470	CRY1 (CRYPTOCHROME 1)	Encodes CRY1, a flavin-type blue-light photoreceptor with ATP binding and autophosphorylation activity. The photoreceptor may be involved in electron transport. Mutant phenotype displays a blue light-dependent inhibition of hypocotyl elongation. Photoreceptor activity requires light-induced homodimerisation of the N-terminal CNT1 domains of CRY1. Involved in blue-light induced stomatal opening. The C-terminal domain of the protein undergoes a light dependent conformational change. Also involved in response to circadian rhythm. Mutants exhibit long hypocotyl under blue light and are out of phase in their response to circadian rhythm. CRY1 is present in the nucleus and cytoplasm. Different subcellular pools of CRY1 have different functions during photomorphogenesis of Arabidopsis seedlings.	O.I.	C.G.	H.G.
8.7	99.0	246.8	At1g11260	837667	STP1 (SUGAR TRANSPORTER 1)	Encodes a H+/hexose cotransporter.	O.I.	C.G.	H.G.
8.6	99.0	263.2	At5g49360	834996	BXL1 (BETA-XYLOSIDASE 1)	Encodes a bifunctional {beta}-D-xylosidase/{alpha}-L-arabinofuranosidase required for pectic arabinan modification. Located in the extracellular matrix. Gene is expressed specifically in tissues undergoing secondary wall thickening. This is a member of glycosyl hydrolase family 3 and has six other closely related members.	O.I.	C.G.	H.G.
8.6	99.0	84.9	At5g63800	836500	MUM2 (MUCILAGE-MODIFIED 2)	Involved in mucilage formation. Mutants form columella and outer cell wall architecture of the mucilage cells resembles wild-type. However, mum2 seeds completely lack seed coat mucilage. This mutation appears to represent a later step in the development of this cell-type. Encodes a beta-galactosidase involved in seed coat mucilage biosynthesis. Member of Glycoside Hydrolase Family 35	O.I.	C.G.	H.G.

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GSM ID	GSM128657
Assay name	Underwood_1-10_Mock-Inoculum-24h_Rep1_ATH1
GSE experiment	GSE5520: Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction

Microarray experiments to specifically-expressed genes

GSM ID GSM128657 Assay name Underwood_1-10_Mock-Inoculum-24h_Rep1_ATH1 GSE experiment GSE5520: Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction

GSM ID GSM128657

Assay name Underwood_1-10_Mock-Inoculum-24h_Rep1_ATH1

GSE experiment GSE5520: Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction