CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM128651

Assay name Underwood_1-4_Cor-hrpS-10e6-24h_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
41.9 99.8 93.8 At4g38860 830041 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. C.G. H.G.
31.6 99.7 38.6 At3g50750 824239 brassinosteroid signalling positive regulator-related F:transcription regulator activity;P:biological_process unknown;C:vacuole;OPFMB O.I. C.G. H.G.
23.8 99.6 42.2 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.
23.2 99.6 78.9 At3g13062 820493 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO O.I. C.G. H.G.
20.4 99.6 31.8 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.
18.9 99.5 118.7 At3g54500 824615 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB O.I. C.G. H.G.
18.7 99.5 127.9 At4g13830 827017 J20 (DNAJ-LIKE 20) DnaJ-like protein (J20); nuclear gene O.I. C.G. H.G.
18.0 99.5 67.8 At2g28630 817412 KCS12 (3-KETOACYL-COA SYNTHASE 12) Encodes KCS12, a member of the 3-ketoacyl-CoA synthase family involved in the biosynthesis of VLCFA (very long chain fatty acids). O.I. C.G. H.G.
18.0 99.5 29.2 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.
17.8 99.5 50.9 At1g18620 838443 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBV O.I. C.G. H.G.
17.7 99.5 15.8 At1g75250 843862 ATRL6 (ARABIDOPSIS RAD-LIKE 6) F:transcription factor activity;P:regulation of transcription;C:unknown;PMO O.I. C.G. H.G.
17.3 99.5 292.1 At3g13750 820584 BGAL1 (Beta galactosidase 1) beta-galactosidase, glycosyl hydrolase family 35 O.I. C.G. H.G.
16.1 99.5 29.5 At2g42040 818804 - F:molecular_function unknown;P:biological_process unknown;C:unknown;PMO O.I. C.G. H.G.
16.0 99.5 22.1 At2g15080 815997 AtRLP19 (Receptor Like Protein 19) F:protein binding, kinase activity;P:signal transduction, defense response;C:endomembrane system;PMOBFAV O.I. C.G. H.G.
16.0 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.
15.0 99.4 47.4 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.
14.9 99.4 79.3 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.
14.8 99.4 106.6 At3g03470 821250 CYP89A9 member of CYP89A O.I. C.G. H.G.
14.8 99.4 34.9 At5g27950 832864 kinesin motor protein-related F:microtubule motor activity, ATP binding;P:microtubule-based movement;C:microtubule associated complex;MOFPB O.I. C.G. H.G.
14.6 99.4 140.9 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.
14.6 99.4 39.7 At1g16260 838195 protein kinase family protein F:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system, integral to membrane;MPOBFVA O.I. C.G. H.G.
14.3 99.4 152.7 At5g16030 831460 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPVBA O.I. C.G. H.G.
14.1 99.4 94.3 At3g02380 821298 COL2 (constans-like 2) homologous to the flowering-time gene CONSTANS (CO) encoding zinc-finger proteins O.I. C.G. H.G.
14.1 99.4 38.1 At3g61210 825293 embryo-abundant protein-related F:unknown;P:unknown;C:cellular_component unknown;BPFOMA O.I. C.G. H.G.
13.8 99.4 104.4 At2g30600 817610 BTB/POZ domain-containing protein F:protein binding;P:cell adhesion;C:cellular_component unknown;MPOVF O.I. C.G. H.G.
13.5 99.4 48.7 At4g08470 826406 MAPKKK10 member of MEKK subfamily O.I. C.G. H.G.
13.5 99.4 33.9 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.
13.4 99.4 90.3 At5g15410 831393 DND1 (DEFENSE NO DEATH 1) 'defense, no death' gene (DND1) encodes a mutated cyclic nucleotide-gated cation channel; Same as CNGC2 (article ID 229): Cyclic nucleotide gated channel, activated by cAMP, conducts K+ and other monovalent cations but excludes Na+, does not contain the GYG amino acid sequence found in other channels with this conductivity profile. Conducts Ca2+ into cells which is linked to the generation of NO and the NO signaling pathway involved in the innate immune response to pathogens. O.I. C.G. H.G.
13.4 99.4 17.3 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.
13.1 99.4 109.8 At5g06980 830589 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POM O.I. C.G. H.G.
13.0 99.4 121.3 At5g21170 832243 5'-AMP-activated protein kinase beta-2 subunit, putative F:AMP-activated protein kinase activity;P:N-terminal protein myristoylation;C:chloroplast;MFPOB O.I. C.G. H.G.
13.0 99.4 52.0 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.
13.0 99.4 49.9 At2g43010 818903 PIF4 (phytochrome interacting factor 4) Isolated as a semidominant mutation defective in red -light responses. Encodes a nuclear localized bHLH protein that interacts with active PhyB protein. Negatively regulates phyB mediated red light responses. Involved in shade avoidance response. Protein abundance is negatively regulated by PhyB. O.I. C.G. H.G.
12.8 99.3 46.5 At5g59080 836025 unknown protein F:molecular_function unknown;P:response to oxidative stress;C:chloroplast;P O.I. C.G. H.G.
12.7 99.3 38.6 At3g03870 821099 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM O.I. C.G. H.G.
12.6 99.3 70.0 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.
12.4 99.3 83.2 At2g15580 816051 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFBV O.I. C.G. H.G.
12.2 99.3 22.4 At3g26220 822223 CYP71B3 cytochrome P450 monooxygenase O.I. C.G. H.G.
12.1 99.3 5.1 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.
12.0 99.3 36.1 At4g27710 828885 CYP709B3 member of CYP709B O.I. C.G. H.G.
11.8 99.3 218.9 At1g69530 843288 ATEXPA1 (ARABIDOPSIS THALIANA EXPANSIN A1) Member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana. O.I. C.G. H.G.
11.6 99.3 96.9 At4g19420 827683 pectinacetylesterase family protein F:carboxylesterase activity;P:biological_process unknown;C:endomembrane system;PMOBA O.I. C.G. H.G.
11.4 99.3 134.1 At1g52190 841649 proton-dependent oligopeptide transport (POT) family protein F:transporter activity;P:oligopeptide transport;C:membrane;PBMFO O.I. C.G. H.G.
11.4 99.3 39.8 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.
11.3 99.3 80.3 At5g60850 836206 OBP4 Encodes a zinc finger protein. O.I. C.G. H.G.
10.9 99.2 375.6 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.
10.9 99.2 110.1 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.
10.8 99.2 186.8 At5g05690 830453 CPD (CONSTITUTIVE PHOTOMORPHOGENIC DWARF) Encodes a member of the CP90A family, a cytochrome P450 monooxygenase which converts 6-deoxocathasterone to 6-deoxoteasterone in the late C6 oxidation pathway and cathasterone to teasterone in the early C6 oxidation pathway of brassinolide biosynthesis. Expressed in cotyledons and leaves. Mutants display de-etiolation and derepression of light-induced genes in the dark, dwarfism, male sterility and activation of stress-regulated genes in the light. The expression of the gene using a CPD promoter:LUC fusion construct was shown to be under circadian and light control. Additionally, the circadian regulation was shown to be independent of BR levels as it remains unchanged in bri1 mutant lines. CPD appears to be involved in the autonomous pathway that regulates the transition to flowering, primarily through a BRI1-mediated signaling pathway that affects FLC expression levels, as uncovered by double mutant analyses. O.I. C.G. H.G.
10.8 99.2 124.6 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.
10.8 99.2 106.1 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.
10.8 99.2 78.7 At3g59060 825075 PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6) Encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. Involved in shade avoidance. Functions as negative regulator of PhyB. Protein levels are modulated by phytochrome B. O.I. C.G. H.G.
10.6 99.2 265.5 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.
10.6 99.2 11.5 At4g00955 827942 - F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PM O.I. C.G. H.G.
10.5 99.2 58.0 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.
10.5 99.2 26.7 At2g25000 817039 WRKY60 Pathogen-induced transcription factor. Forms protein complexes with itself and with WRKY40. Coexpression with WRKY18 or WRKY40 made plants more susceptible to both P. syringae and B. cinerea. WRKY18, WRKY40, and WRKY60 have partially redundant roles in response to the hemibiotrophic bacterial pathogen Pseudomonas syringae and the necrotrophic fungal pathogen Botrytis cinerea, with WRKY18 playing a more important role than the other two. O.I. C.G. H.G.
10.0 99.2 51.5 At4g30993 829225 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
9.9 99.1 380.4 At4g35770 829730 SEN1 (SENESCENCE 1) Senescence-associated gene that is strongly induced by phosphate starvation. Transcripts are differentially regulated at the level of mRNA stability at different times of day. mRNAs are targets of the mRNA degradation pathway mediated by the downstream (DST) instability determinant. O.I. C.G. H.G.
9.9 99.1 49.9 At3g57410 824908 VLN3 (VILLIN 3) Encodes a protein with high homology to animal villin. O.I. C.G. H.G.
9.7 99.1 279.3 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.
9.7 99.1 139.1 At5g40450 834043 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast, plasma membrane;MOBFPAV O.I. C.G. H.G.
9.6 99.1 431.7 At1g64720 842780 CP5 membrane related protein CP5 O.I. C.G. H.G.
9.5 99.1 55.5 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.
9.5 99.1 51.4 At5g28770 832990 BZO2H3 bZIP protein BZO2H3 mRNA, partial cds O.I. C.G. H.G.
9.5 99.1 42.4 At5g22510 832312 beta-fructofuranosidase, putative / invertase, putative / saccharase, putative / beta-fructosidase, putative F:catalytic activity, beta-fructofuranosidase activity;P:biological_process unknown;C:chloroplast;OPB O.I. C.G. H.G.
9.5 99.1 28.7 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.
9.4 99.1 39.4 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.
9.3 99.1 48.9 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.
9.3 99.1 28.0 At3g57800 825530 basic helix-loop-helix (bHLH) family protein F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PMFB O.I. C.G. H.G.
9.2 99.1 64.0 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.
9.1 99.1 165.0 At2g39570 818542 ACT domain-containing protein F:amino acid binding;P:metabolic process;C:unknown;POB O.I. C.G. H.G.
8.9 99.0 27.7 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.
8.8 99.0 116.5 At1g80180 844358 unknown protein F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;P O.I. C.G. H.G.
8.8 99.0 72.7 At3g12320 820411 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. C.G. H.G.
8.8 99.0 34.7 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.
8.7 99.0 37.2 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.
8.6 99.0 94.8 At3g60320 825203 DNA binding F:DNA binding;P:biological_process unknown;C:cellular_component unknown;OMPFBVA 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.
41.9	99.8	93.8	At4g38860	830041	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	C.G.	H.G.
31.6	99.7	38.6	At3g50750	824239	brassinosteroid signalling positive regulator-related	F:transcription regulator activity;P:biological_process unknown;C:vacuole;OPFMB	O.I.	C.G.	H.G.
23.8	99.6	42.2	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.
23.2	99.6	78.9	At3g13062	820493	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO	O.I.	C.G.	H.G.
20.4	99.6	31.8	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.
18.9	99.5	118.7	At3g54500	824615	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB	O.I.	C.G.	H.G.
18.7	99.5	127.9	At4g13830	827017	J20 (DNAJ-LIKE 20)	DnaJ-like protein (J20); nuclear gene	O.I.	C.G.	H.G.
18.0	99.5	67.8	At2g28630	817412	KCS12 (3-KETOACYL-COA SYNTHASE 12)	Encodes KCS12, a member of the 3-ketoacyl-CoA synthase family involved in the biosynthesis of VLCFA (very long chain fatty acids).	O.I.	C.G.	H.G.
18.0	99.5	29.2	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.
17.8	99.5	50.9	At1g18620	838443	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBV	O.I.	C.G.	H.G.
17.7	99.5	15.8	At1g75250	843862	ATRL6 (ARABIDOPSIS RAD-LIKE 6)	F:transcription factor activity;P:regulation of transcription;C:unknown;PMO	O.I.	C.G.	H.G.
17.3	99.5	292.1	At3g13750	820584	BGAL1 (Beta galactosidase 1)	beta-galactosidase, glycosyl hydrolase family 35	O.I.	C.G.	H.G.
16.1	99.5	29.5	At2g42040	818804	-	F:molecular_function unknown;P:biological_process unknown;C:unknown;PMO	O.I.	C.G.	H.G.
16.0	99.5	22.1	At2g15080	815997	AtRLP19 (Receptor Like Protein 19)	F:protein binding, kinase activity;P:signal transduction, defense response;C:endomembrane system;PMOBFAV	O.I.	C.G.	H.G.
16.0	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.
15.0	99.4	47.4	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.
14.9	99.4	79.3	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.
14.8	99.4	106.6	At3g03470	821250	CYP89A9	member of CYP89A	O.I.	C.G.	H.G.
14.8	99.4	34.9	At5g27950	832864	kinesin motor protein-related	F:microtubule motor activity, ATP binding;P:microtubule-based movement;C:microtubule associated complex;MOFPB	O.I.	C.G.	H.G.
14.6	99.4	140.9	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.
14.6	99.4	39.7	At1g16260	838195	protein kinase family protein	F:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system, integral to membrane;MPOBFVA	O.I.	C.G.	H.G.
14.3	99.4	152.7	At5g16030	831460	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPVBA	O.I.	C.G.	H.G.
14.1	99.4	94.3	At3g02380	821298	COL2 (constans-like 2)	homologous to the flowering-time gene CONSTANS (CO) encoding zinc-finger proteins	O.I.	C.G.	H.G.
14.1	99.4	38.1	At3g61210	825293	embryo-abundant protein-related	F:unknown;P:unknown;C:cellular_component unknown;BPFOMA	O.I.	C.G.	H.G.
13.8	99.4	104.4	At2g30600	817610	BTB/POZ domain-containing protein	F:protein binding;P:cell adhesion;C:cellular_component unknown;MPOVF	O.I.	C.G.	H.G.
13.5	99.4	48.7	At4g08470	826406	MAPKKK10	member of MEKK subfamily	O.I.	C.G.	H.G.
13.5	99.4	33.9	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.
13.4	99.4	90.3	At5g15410	831393	DND1 (DEFENSE NO DEATH 1)	'defense, no death' gene (DND1) encodes a mutated cyclic nucleotide-gated cation channel; Same as CNGC2 (article ID 229): Cyclic nucleotide gated channel, activated by cAMP, conducts K+ and other monovalent cations but excludes Na+, does not contain the GYG amino acid sequence found in other channels with this conductivity profile. Conducts Ca2+ into cells which is linked to the generation of NO and the NO signaling pathway involved in the innate immune response to pathogens.	O.I.	C.G.	H.G.
13.4	99.4	17.3	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.
13.1	99.4	109.8	At5g06980	830589	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POM	O.I.	C.G.	H.G.
13.0	99.4	121.3	At5g21170	832243	5'-AMP-activated protein kinase beta-2 subunit, putative	F:AMP-activated protein kinase activity;P:N-terminal protein myristoylation;C:chloroplast;MFPOB	O.I.	C.G.	H.G.
13.0	99.4	52.0	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.
13.0	99.4	49.9	At2g43010	818903	PIF4 (phytochrome interacting factor 4)	Isolated as a semidominant mutation defective in red -light responses. Encodes a nuclear localized bHLH protein that interacts with active PhyB protein. Negatively regulates phyB mediated red light responses. Involved in shade avoidance response. Protein abundance is negatively regulated by PhyB.	O.I.	C.G.	H.G.
12.8	99.3	46.5	At5g59080	836025	unknown protein	F:molecular_function unknown;P:response to oxidative stress;C:chloroplast;P	O.I.	C.G.	H.G.
12.7	99.3	38.6	At3g03870	821099	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM	O.I.	C.G.	H.G.
12.6	99.3	70.0	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.
12.4	99.3	83.2	At2g15580	816051	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFBV	O.I.	C.G.	H.G.
12.2	99.3	22.4	At3g26220	822223	CYP71B3	cytochrome P450 monooxygenase	O.I.	C.G.	H.G.
12.1	99.3	5.1	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.
12.0	99.3	36.1	At4g27710	828885	CYP709B3	member of CYP709B	O.I.	C.G.	H.G.
11.8	99.3	218.9	At1g69530	843288	ATEXPA1 (ARABIDOPSIS THALIANA EXPANSIN A1)	Member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, Plant Mol Bio). Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana.	O.I.	C.G.	H.G.
11.6	99.3	96.9	At4g19420	827683	pectinacetylesterase family protein	F:carboxylesterase activity;P:biological_process unknown;C:endomembrane system;PMOBA	O.I.	C.G.	H.G.
11.4	99.3	134.1	At1g52190	841649	proton-dependent oligopeptide transport (POT) family protein	F:transporter activity;P:oligopeptide transport;C:membrane;PBMFO	O.I.	C.G.	H.G.
11.4	99.3	39.8	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.
11.3	99.3	80.3	At5g60850	836206	OBP4	Encodes a zinc finger protein.	O.I.	C.G.	H.G.
10.9	99.2	375.6	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.
10.9	99.2	110.1	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.
10.8	99.2	186.8	At5g05690	830453	CPD (CONSTITUTIVE PHOTOMORPHOGENIC DWARF)	Encodes a member of the CP90A family, a cytochrome P450 monooxygenase which converts 6-deoxocathasterone to 6-deoxoteasterone in the late C6 oxidation pathway and cathasterone to teasterone in the early C6 oxidation pathway of brassinolide biosynthesis. Expressed in cotyledons and leaves. Mutants display de-etiolation and derepression of light-induced genes in the dark, dwarfism, male sterility and activation of stress-regulated genes in the light. The expression of the gene using a CPD promoter:LUC fusion construct was shown to be under circadian and light control. Additionally, the circadian regulation was shown to be independent of BR levels as it remains unchanged in bri1 mutant lines. CPD appears to be involved in the autonomous pathway that regulates the transition to flowering, primarily through a BRI1-mediated signaling pathway that affects FLC expression levels, as uncovered by double mutant analyses.	O.I.	C.G.	H.G.
10.8	99.2	124.6	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.
10.8	99.2	106.1	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.
10.8	99.2	78.7	At3g59060	825075	PIL6 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 6)	Encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. Involved in shade avoidance. Functions as negative regulator of PhyB. Protein levels are modulated by phytochrome B.	O.I.	C.G.	H.G.
10.6	99.2	265.5	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.
10.6	99.2	11.5	At4g00955	827942	-	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PM	O.I.	C.G.	H.G.
10.5	99.2	58.0	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.
10.5	99.2	26.7	At2g25000	817039	WRKY60	Pathogen-induced transcription factor. Forms protein complexes with itself and with WRKY40. Coexpression with WRKY18 or WRKY40 made plants more susceptible to both P. syringae and B. cinerea. WRKY18, WRKY40, and WRKY60 have partially redundant roles in response to the hemibiotrophic bacterial pathogen Pseudomonas syringae and the necrotrophic fungal pathogen Botrytis cinerea, with WRKY18 playing a more important role than the other two.	O.I.	C.G.	H.G.
10.0	99.2	51.5	At4g30993	829225	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
9.9	99.1	380.4	At4g35770	829730	SEN1 (SENESCENCE 1)	Senescence-associated gene that is strongly induced by phosphate starvation. Transcripts are differentially regulated at the level of mRNA stability at different times of day. mRNAs are targets of the mRNA degradation pathway mediated by the downstream (DST) instability determinant.	O.I.	C.G.	H.G.
9.9	99.1	49.9	At3g57410	824908	VLN3 (VILLIN 3)	Encodes a protein with high homology to animal villin.	O.I.	C.G.	H.G.
9.7	99.1	279.3	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.
9.7	99.1	139.1	At5g40450	834043	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast, plasma membrane;MOBFPAV	O.I.	C.G.	H.G.
9.6	99.1	431.7	At1g64720	842780	CP5	membrane related protein CP5	O.I.	C.G.	H.G.
9.5	99.1	55.5	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.
9.5	99.1	51.4	At5g28770	832990	BZO2H3	bZIP protein BZO2H3 mRNA, partial cds	O.I.	C.G.	H.G.
9.5	99.1	42.4	At5g22510	832312	beta-fructofuranosidase, putative / invertase, putative / saccharase, putative / beta-fructosidase, putative	F:catalytic activity, beta-fructofuranosidase activity;P:biological_process unknown;C:chloroplast;OPB	O.I.	C.G.	H.G.
9.5	99.1	28.7	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.
9.4	99.1	39.4	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.
9.3	99.1	48.9	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.
9.3	99.1	28.0	At3g57800	825530	basic helix-loop-helix (bHLH) family protein	F:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PMFB	O.I.	C.G.	H.G.
9.2	99.1	64.0	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.
9.1	99.1	165.0	At2g39570	818542	ACT domain-containing protein	F:amino acid binding;P:metabolic process;C:unknown;POB	O.I.	C.G.	H.G.
8.9	99.0	27.7	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.
8.8	99.0	116.5	At1g80180	844358	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;P	O.I.	C.G.	H.G.
8.8	99.0	72.7	At3g12320	820411	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	C.G.	H.G.
8.8	99.0	34.7	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.
8.7	99.0	37.2	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.
8.6	99.0	94.8	At3g60320	825203	DNA binding	F:DNA binding;P:biological_process unknown;C:cellular_component unknown;OMPFBVA	O.I.	C.G.	H.G.

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GSM ID	GSM128651
Assay name	Underwood_1-4_Cor-hrpS-10e6-24h_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 GSM128651 Assay name Underwood_1-4_Cor-hrpS-10e6-24h_Rep1_ATH1 GSE experiment GSE5520: Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction

GSM ID GSM128651

Assay name Underwood_1-4_Cor-hrpS-10e6-24h_Rep1_ATH1

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