CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM128650

Assay name Underwood_1-3_Cor-10e6-24h_Rep3_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
56.2 99.8 178.7 At5g60850 836206 OBP4 Encodes a zinc finger protein. O.I. C.G. H.G.
52.2 99.8 68.1 At3g15780 820821 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. C.G. H.G.
36.7 99.7 38.2 At1g08230 837344 - - O.I. C.G. H.G.
34.1 99.7 63.3 At3g03870 821099 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM O.I. C.G. H.G.
33.0 99.7 140.9 At3g12320 820411 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. C.G. H.G.
32.5 99.7 65.5 At3g61630 825336 CRF6 (CYTOKININ RESPONSE FACTOR 6) CRF6 encodes one of the six cytokinin response factors. CRF5 belongs to the AP2/ERF superfamily of the transcriptional factors. CRF proteins rapidly relocalize to the nucleus in response to cytokinin. Analysis of loos-of-function mutants revealed that the CRFs function redundantly to regulate the development of embryos, cotyledons and leaves. O.I. C.G. H.G.
31.7 99.7 42.0 At1g01990 837456 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
31.0 99.7 19.3 At1g35560 840452 TCP family transcription factor, putative F:transcription factor activity;P:regulation of transcription;C:chloroplast;PMOF O.I. C.G. H.G.
30.8 99.7 16.3 At3g09600 820117 myb family transcription factor F:transcription factor activity, DNA binding;P:in 9 processes;C:chloroplast;PMOF O.I. C.G. H.G.
30.1 99.7 20.2 At5g04880 3770684 - pseudogene of ABC transporter family protein O.I. C.G. H.G.
29.2 99.7 88.2 At3g60910 825262 catalytic/ methyltransferase F:methyltransferase activity, catalytic activity;P:metabolic process;C:cellular_component unknown;BMOPFA O.I. C.G. H.G.
29.1 99.7 76.0 At1g27650 839657 ATU2AF35A U2 auxiliary factor small subunit. The atU2AF35a protein and its homolog, atU2AF35b, contain most of the conserved domains of hsU2AF35, including the psiRRM, one RS domain, two zinc fingers, and the two regions for interacting with U2AF large subunit. Both proteins lack the stretch of glycines present in human U2AF35. The sequences are overall 83% identical, and each Arabidopsis homolog shows approximately 70% similarity to hsU2AF35. U2AF(35) homologs were also identified from maize, rice and other plants with large-scale EST projects. Both genes are expressed in all major tissues, with atU2AF(35)a expressed at a higher level than atU2AF(35)b in most tissues. The expression patterns were different in roots: atU2AF(35)b expressed strongly in whole young roots and root tips and atU2AF(35)a limited to root vascular regions. O.I. C.G. H.G.
27.7 99.7 36.2 At3g50750 824239 brassinosteroid signalling positive regulator-related F:transcription regulator activity;P:biological_process unknown;C:vacuole;OPFMB O.I. C.G. H.G.
27.0 99.7 42.0 At4g00335 828093 RHB1A F:protein binding, zinc ion binding;P:N-terminal protein myristoylation;C:unknown;PMOFV O.I. C.G. H.G.
27.0 99.7 32.7 At5g03560 831789 nucleobase:cation symporter F:nucleobase:cation symporter activity;P:biological_process unknown;C:cellular_component unknown;BMFPO O.I. C.G. H.G.
25.7 99.7 96.6 At4g03030 828110 kelch repeat-containing F-box family protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;MPOBVF O.I. C.G. H.G.
25.7 99.7 69.0 At5g64280 836549 DiT2.2 (dicarboxylate transporter 2.2) F:oxoglutarate:malate antiporter activity;P:malate transport, sodium ion transport;C:chloroplast, membrane;BOPAFMV O.I. C.G. H.G.
25.4 99.6 35.9 At5g22390 832300 unknown protein F:unknown;P:unknown;C:unknown;PMOF O.I. C.G. H.G.
24.7 99.6 73.7 At1g33110 840207 MATE efflux family protein F:antiporter activity, drug transporter activity, transporter activity;P:multidrug transport;C:membrane;BOPFMA O.I. C.G. H.G.
23.9 99.6 33.6 At4g08330 826387 unknown protein F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;P O.I. C.G. H.G.
23.4 99.6 60.4 At5g17300 831595 myb family transcription factor F:transcription factor activity;P:regulation of transcription;C:unknown;PMOFVB O.I. C.G. H.G.
23.4 99.6 39.4 At2g46610 819273 arginine/serine-rich splicing factor, putative F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFOBVA O.I. C.G. H.G.
22.3 99.6 78.6 At4g15780 827258 ATVAMP724 member of VAMP72 Gene Family O.I. C.G. H.G.
22.2 99.6 61.6 At5g47610 834811 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFV O.I. C.G. H.G.
22.0 99.6 177.9 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.
21.8 99.6 43.3 At1g76110 843943 high mobility group (HMG1/2) family protein / ARID/BRIGHT DNA-binding domain-containing protein F:transcription factor activity;P:regulation of transcription;C:intracellular, nucleus;MOFP O.I. C.G. H.G.
21.6 99.6 17.0 At4g36870 829840 BLH2 (BEL1-LIKE HOMEODOMAIN 2) Encodes a member of the BEL family of homeodomain proteins. Plants doubly mutant for saw1/saw2 (blh2/blh4) have serrated leaves. BP is expressed in the serrated leaves, therefore saw1/saw2 may act redundantly to repress BP in leaves. O.I. C.G. H.G.
21.5 99.6 222.2 At1g78020 844137 senescence-associated protein-related F:unknown;P:unknown;C:unknown;P O.I. C.G. H.G.
21.5 99.6 65.7 At1g76460 843979 RNA recognition motif (RRM)-containing protein F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFOBA O.I. C.G. H.G.
21.3 99.6 42.1 At3g04000 819555 short-chain dehydrogenase/reductase (SDR) family protein F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:unknown;BOMFPAV O.I. C.G. H.G.
20.9 99.6 111.4 At4g27990 828912 YGGT family protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast envelope;BOP O.I. C.G. H.G.
20.4 99.6 123.0 At3g54500 824615 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB O.I. C.G. H.G.
20.2 99.6 51.0 At1g02100 837541 leucine carboxyl methyltransferase family protein F:methyltransferase activity;P:biological_process unknown;C:cellular_component unknown;FMOP O.I. C.G. H.G.
19.6 99.6 157.2 At5g54080 835494 HGO (HOMOGENTISATE 1,2-DIOXYGENASE) homogentisate 1,2-dioxygenase O.I. C.G. H.G.
19.4 99.6 49.8 At4g31080 829235 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPO O.I. C.G. H.G.
19.3 99.6 114.7 At5g56140 835713 KH domain-containing protein F:RNA binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPBOFVA O.I. C.G. H.G.
19.3 99.6 88.0 At5g15850 831442 COL1 (constans-like 1) Homologous to the flowering-time gene CONSTANS. O.I. C.G. H.G.
19.2 99.6 33.4 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.
18.8 99.5 119.9 At3g03470 821250 CYP89A9 member of CYP89A O.I. C.G. H.G.
18.7 99.5 71.2 At5g01240 831866 amino acid permease, putative F:transporter activity;P:amino acid transport;C:membrane;PFMO O.I. C.G. H.G.
18.7 99.5 54.2 At3g01560 821110 proline-rich family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBVA O.I. C.G. H.G.
18.6 99.5 142.6 At1g07350 837246 transformer serine/arginine-rich ribonucleoprotein, putative F:RNA binding, nucleotide binding, nucleic acid binding;P:RNA splicing;C:unknown;MPFOBVA O.I. C.G. H.G.
18.5 99.5 87.3 At1g13380 837898 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
18.5 99.5 24.8 At3g11100 820281 transcription factor F:transcription factor activity;P:regulation of transcription;C:nucleus;POMFBA O.I. C.G. H.G.
18.4 99.5 182.7 At2g20920 816626 unknown protein F:unknown;P:unknown;C:membrane;BPO O.I. C.G. H.G.
18.2 99.5 100.5 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.
18.1 99.5 35.3 At1g01725 839271 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
18.0 99.5 56.8 At1g71480 843489 nuclear transport factor 2 (NTF2) family protein F:protein transporter activity;P:transport, protein import into nucleus;C:chloroplast thylakoid membrane, nucleus, intracellular, chloroplast;PBO O.I. C.G. H.G.
18.0 99.5 15.9 At1g75250 843862 ATRL6 (ARABIDOPSIS RAD-LIKE 6) F:transcription factor activity;P:regulation of transcription;C:unknown;PMO O.I. C.G. H.G.
17.6 99.5 124.0 At4g13830 827017 J20 (DNAJ-LIKE 20) DnaJ-like protein (J20); nuclear gene O.I. C.G. H.G.
17.5 99.5 80.3 At3g62190 825392 DNAJ heat shock N-terminal domain-containing protein F:heat shock protein binding;P:protein folding;C:cellular_component unknown;OBMPFA O.I. C.G. H.G.
17.5 99.5 45.4 At3g60080 825178 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.
17.1 99.5 49.1 At5g20380 832160 PHT4 Encodes an inorganic phosphate transporter (PHT4;5). O.I. C.G. H.G.
17.1 99.5 15.4 At5g67190 836854 AP2 domain-containing transcription factor, putative encodes a member of the DREB subfamily A-5 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 16 members in this subfamily including RAP2.1, RAP2.9 and RAP2.10. O.I. C.G. H.G.
17.0 99.5 28.3 At3g01850 821068 ribulose-phosphate 3-epimerase, cytosolic, putative / pentose-5-phosphate 3-epimerase, putative F:ribulose-phosphate 3-epimerase activity, catalytic activity;P:carbohydrate metabolic process, metabolic process;C:endomembrane system;OBMFPA O.I. C.G. H.G.
16.9 99.5 34.7 At5g57360 835842 ZTL (ZEITLUPE) Encodes clock-associated PAS protein ZTL; Also known as FKF1-like protein 2 or ADAGIO1(ADO1). A protein containing a PAS domain ZTL contributes to the plant fitness (carbon fixation, biomass) by influencing the circadian clock period. ZTL is the F-box component of an SCF complex implicated in the degradation of TOC1. O.I. C.G. H.G.
16.9 99.5 26.3 At3g28080 822432 nodulin MtN21 family protein F:molecular_function unknown;P:biological_process unknown;C:membrane;PBOAM O.I. C.G. H.G.
16.8 99.5 47.6 At2g21950 816731 SKIP6 (SKP1 interacting partner 6) Encodes an SKP1 interacting partner (SKIP6). O.I. C.G. H.G.
16.6 99.5 46.9 At3g07870 819978 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. C.G. H.G.
16.5 99.5 62.5 At4g26480 828754 KH domain-containing protein F:nicotianamine synthase activity, RNA binding, nucleic acid binding;P:nicotianamine biosynthetic process;C:cellular_component unknown;MPFOB O.I. C.G. H.G.
16.3 99.5 64.9 At1g80310 844371 sulfate transmembrane transporter F:sulfate transmembrane transporter activity;P:response to salt stress;C:vacuole;BOPFMA O.I. C.G. H.G.
15.9 99.5 39.7 At4g36780 829831 transcription regulator F:transcription regulator activity;P:biological_process unknown;C:cellular_component unknown;PF O.I. C.G. H.G.
15.8 99.5 54.8 At3g04350 819590 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFMBO O.I. C.G. H.G.
15.6 99.5 60.2 At1g62960 842598 ACS10 (ACC SYNTHASE 10) Encodes an aminotransferase with broad specificity for aspartate and aromatic amino aids such as tyrosine and phenylalanine. It does not act on branched chain amino acids and does not have ACC synthase activity. O.I. C.G. H.G.
15.5 99.5 137.7 At3g07560 819945 PEX13 (PEROXIN 13) Encodes peroxin 13 (PEX13) involved in protein transport into peroxisomes. O.I. C.G. H.G.
15.5 99.5 69.8 At2g45620 819170 nucleotidyltransferase family protein F:nucleotidyltransferase activity;P:biological_process unknown;C:cellular_component unknown;MOFPB O.I. C.G. H.G.
15.5 99.5 57.0 At4g38860 830041 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. C.G. H.G.
15.4 99.5 122.1 At1g19350 838518 BES1 (BRI1-EMS-SUPPRESSOR 1) Encodes brassinosteroid (BR) signalling protein that accumulates in the nucleus as dephosphorylated form in response to BRs. Is phosphorylated by the BIN2 GSK3 kinase. It synergistically interacts with BIM1 to bind to E box sequences (CANNTG). The protein contains a nuclear localization signal (NLS), followed by a highly conserved amino-terminal domain (N) shared by all family members, a BIN2 phosphorylation domain (P), a PEST motif, involved in protein degradation in the absence of BR, and a carboxyl-terminal domain. BES1 can interact with the ELF6 and REF6 Jumonji N/C-domain containing proteins and may direct them to modify histone methylation upstream of some brassinosteroid responsive-genes O.I. C.G. H.G.
15.4 99.5 57.1 At2g32530 817814 ATCSLB03 encodes a gene similar to cellulose synthase O.I. C.G. H.G.
15.4 99.5 7.9 At2g35950 818168 EDA12 (embryo sac development arrest 12) F:molecular_function unknown;P:megagametogenesis;C:unknown;P O.I. C.G. H.G.
15.1 99.4 182.1 At2g34590 818024 transketolase family protein F:pyruvate dehydrogenase (acetyl-transferring) activity, transketolase activity;P:pollen tube development;C:chloroplast, chloroplast envelope;BOMPFA O.I. C.G. H.G.
15.0 99.4 219.6 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.
15.0 99.4 197.6 At1g58030 842170 CAT2 (CATIONIC AMINO ACID TRANSPORTER 2) Encodes a member of the cationic amino acid transporter (CAT) subfamily of amino acid polyamine choline transporters. Localized to the tonoplast. O.I. C.G. H.G.
14.9 99.4 59.1 At5g11840 831057 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;OBP O.I. C.G. H.G.
14.9 99.4 30.9 At4g29820 829104 CFIM-25 Encodes a homolog of the protein CFI-25, a polyadenylation factor subunit. O.I. C.G. H.G.
14.8 99.4 65.4 At1g08460 837366 HDA08 F:histone deacetylase activity;P:histone deacetylation;C:cellular_component unknown;OBMFPA O.I. C.G. H.G.
14.7 99.4 38.0 At1g32520 840146 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;MPO O.I. C.G. H.G.
14.7 99.4 25.0 At1g20890 838682 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PMO O.I. C.G. H.G.
14.6 99.4 44.6 At4g17070 827415 peptidyl-prolyl cis-trans isomerase F:peptidyl-prolyl cis-trans isomerase activity;P:response to oxidative stress;C:unknown;PBMO O.I. C.G. H.G.
14.5 99.4 112.9 At3g55460 824712 SCL30 encodes an SC35-like splicing factor that is localized to nuclear specks. O.I. C.G. H.G.
14.0 99.4 33.5 At5g05710 830455 pleckstrin homology (PH) domain-containing protein F:molecular_function unknown;P:unknown;C:cellular_component unknown;MOPFV O.I. C.G. H.G.
13.9 99.4 22.3 At1g48550 841276 vacuolar protein sorting-associated protein 26 family protein / VPS26 family protein F:molecular_function unknown;P:intracellular protein transport, vacuolar transport, retrograde transport, endosome to Golgi;C:retromer complex;MOPF O.I. C.G. H.G.
13.8 99.4 61.5 At2g47960 819408 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;MFOP O.I. C.G. H.G.
13.8 99.4 11.6 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.
13.7 99.4 217.4 At5g16110 831468 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
13.7 99.4 41.4 At2g23760 816908 BLH4 (BEL1-LIKE HOMEODOMAIN 4) Encodes a member of the BEL family of homeodomain proteins. Plants doubly mutant for saw1/saw2 (blh2/blh4) have serrated leaves. BP is expressed in the serrated leaves, therefore saw2 and saw1 may act redundantly to repress BP in leaves. O.I. C.G. H.G.
13.7 99.4 26.5 At5g51170 835191 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPO O.I. C.G. H.G.
13.6 99.4 201.2 At2g39570 818542 ACT domain-containing protein F:amino acid binding;P:metabolic process;C:unknown;POB O.I. C.G. H.G.
13.6 99.4 96.9 At5g22000 832260 RHF2A (RING-H2 GROUP F2A) encodes a RING-type E3 ubiquitin ligase implicated in gametogenesis. Double mutant analyses with RHF1a suggests that RHF2a may be involved in targetting ICK4KRP6 for degradation following meiosis in order to allow the mitoses associated with megagametogenesis and microgametogenesis to occur. RHF2a is expressed in all four floral whorls and is present at ~8-fold higher levels than RHF1a in inflorescences by RT-PCR analyses. O.I. C.G. H.G.
13.6 99.4 38.8 At2g21195 816656 unknown protein F:molecular_function unknown;P:response to oxidative stress;C:cellular_component unknown;P O.I. C.G. H.G.
13.6 99.4 27.2 At1g51360 841560 DABB1 (DIMERIC A/B BARREL DOMAINS-PROTEIN 1) Involved in defense against fungal pathogens and located in cytosol. O.I. C.G. H.G.
13.4 99.4 44.7 At2g33250 817887 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
13.3 99.4 75.1 At2g21185 816654 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. C.G. H.G.
13.3 99.4 47.4 At5g59080 836025 unknown protein F:molecular_function unknown;P:response to oxidative stress;C:chloroplast;P O.I. C.G. H.G.
13.1 99.4 45.8 At5g50520 835120 nodulin family protein F:unknown;P:unknown;C:endomembrane system;BOPFMA O.I. C.G. H.G.
13.1 99.4 42.7 At1g64500 842758 glutaredoxin family protein F:electron carrier activity, protein disulfide oxidoreductase activity;P:N-terminal protein myristoylation, cell redox homeostasis;C:cellular_component unknown;PMBOF O.I. C.G. H.G.
13.1 99.4 39.1 At1g19680 838555 protein binding / zinc ion binding F:protein binding, zinc ion binding;P:N-terminal protein myristoylation;C:unknown;OPMBF O.I. C.G. H.G.
12.9 99.3 94.4 At5g32440 833203 - F:unknown;P:unknown;C:chloroplast;OPMFB O.I. C.G. H.G.
12.9 99.3 33.8 At1g33250 840219 fringe-related protein F:transferase activity, transferring glycosyl groups;P:unknown;C:chloroplast, membrane;MPFO O.I. C.G. H.G.
12.8 99.3 129.3 At1g29970 839876 RPL18AA (60S RIBOSOMAL PROTEIN L18A-1) F:unknown;P:unknown;C:unknown;P 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.
56.2	99.8	178.7	At5g60850	836206	OBP4	Encodes a zinc finger protein.	O.I.	C.G.	H.G.
52.2	99.8	68.1	At3g15780	820821	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	C.G.	H.G.
36.7	99.7	38.2	At1g08230	837344	-	-	O.I.	C.G.	H.G.
34.1	99.7	63.3	At3g03870	821099	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM	O.I.	C.G.	H.G.
33.0	99.7	140.9	At3g12320	820411	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	C.G.	H.G.
32.5	99.7	65.5	At3g61630	825336	CRF6 (CYTOKININ RESPONSE FACTOR 6)	CRF6 encodes one of the six cytokinin response factors. CRF5 belongs to the AP2/ERF superfamily of the transcriptional factors. CRF proteins rapidly relocalize to the nucleus in response to cytokinin. Analysis of loos-of-function mutants revealed that the CRFs function redundantly to regulate the development of embryos, cotyledons and leaves.	O.I.	C.G.	H.G.
31.7	99.7	42.0	At1g01990	837456	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
31.0	99.7	19.3	At1g35560	840452	TCP family transcription factor, putative	F:transcription factor activity;P:regulation of transcription;C:chloroplast;PMOF	O.I.	C.G.	H.G.
30.8	99.7	16.3	At3g09600	820117	myb family transcription factor	F:transcription factor activity, DNA binding;P:in 9 processes;C:chloroplast;PMOF	O.I.	C.G.	H.G.
30.1	99.7	20.2	At5g04880	3770684	-	pseudogene of ABC transporter family protein	O.I.	C.G.	H.G.
29.2	99.7	88.2	At3g60910	825262	catalytic/ methyltransferase	F:methyltransferase activity, catalytic activity;P:metabolic process;C:cellular_component unknown;BMOPFA	O.I.	C.G.	H.G.
29.1	99.7	76.0	At1g27650	839657	ATU2AF35A	U2 auxiliary factor small subunit. The atU2AF35a protein and its homolog, atU2AF35b, contain most of the conserved domains of hsU2AF35, including the psiRRM, one RS domain, two zinc fingers, and the two regions for interacting with U2AF large subunit. Both proteins lack the stretch of glycines present in human U2AF35. The sequences are overall 83% identical, and each Arabidopsis homolog shows approximately 70% similarity to hsU2AF35. U2AF(35) homologs were also identified from maize, rice and other plants with large-scale EST projects. Both genes are expressed in all major tissues, with atU2AF(35)a expressed at a higher level than atU2AF(35)b in most tissues. The expression patterns were different in roots: atU2AF(35)b expressed strongly in whole young roots and root tips and atU2AF(35)a limited to root vascular regions.	O.I.	C.G.	H.G.
27.7	99.7	36.2	At3g50750	824239	brassinosteroid signalling positive regulator-related	F:transcription regulator activity;P:biological_process unknown;C:vacuole;OPFMB	O.I.	C.G.	H.G.
27.0	99.7	42.0	At4g00335	828093	RHB1A	F:protein binding, zinc ion binding;P:N-terminal protein myristoylation;C:unknown;PMOFV	O.I.	C.G.	H.G.
27.0	99.7	32.7	At5g03560	831789	nucleobase:cation symporter	F:nucleobase:cation symporter activity;P:biological_process unknown;C:cellular_component unknown;BMFPO	O.I.	C.G.	H.G.
25.7	99.7	96.6	At4g03030	828110	kelch repeat-containing F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;MPOBVF	O.I.	C.G.	H.G.
25.7	99.7	69.0	At5g64280	836549	DiT2.2 (dicarboxylate transporter 2.2)	F:oxoglutarate:malate antiporter activity;P:malate transport, sodium ion transport;C:chloroplast, membrane;BOPAFMV	O.I.	C.G.	H.G.
25.4	99.6	35.9	At5g22390	832300	unknown protein	F:unknown;P:unknown;C:unknown;PMOF	O.I.	C.G.	H.G.
24.7	99.6	73.7	At1g33110	840207	MATE efflux family protein	F:antiporter activity, drug transporter activity, transporter activity;P:multidrug transport;C:membrane;BOPFMA	O.I.	C.G.	H.G.
23.9	99.6	33.6	At4g08330	826387	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;P	O.I.	C.G.	H.G.
23.4	99.6	60.4	At5g17300	831595	myb family transcription factor	F:transcription factor activity;P:regulation of transcription;C:unknown;PMOFVB	O.I.	C.G.	H.G.
23.4	99.6	39.4	At2g46610	819273	arginine/serine-rich splicing factor, putative	F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFOBVA	O.I.	C.G.	H.G.
22.3	99.6	78.6	At4g15780	827258	ATVAMP724	member of VAMP72 Gene Family	O.I.	C.G.	H.G.
22.2	99.6	61.6	At5g47610	834811	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFV	O.I.	C.G.	H.G.
22.0	99.6	177.9	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.
21.8	99.6	43.3	At1g76110	843943	high mobility group (HMG1/2) family protein / ARID/BRIGHT DNA-binding domain-containing protein	F:transcription factor activity;P:regulation of transcription;C:intracellular, nucleus;MOFP	O.I.	C.G.	H.G.
21.6	99.6	17.0	At4g36870	829840	BLH2 (BEL1-LIKE HOMEODOMAIN 2)	Encodes a member of the BEL family of homeodomain proteins. Plants doubly mutant for saw1/saw2 (blh2/blh4) have serrated leaves. BP is expressed in the serrated leaves, therefore saw1/saw2 may act redundantly to repress BP in leaves.	O.I.	C.G.	H.G.
21.5	99.6	222.2	At1g78020	844137	senescence-associated protein-related	F:unknown;P:unknown;C:unknown;P	O.I.	C.G.	H.G.
21.5	99.6	65.7	At1g76460	843979	RNA recognition motif (RRM)-containing protein	F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFOBA	O.I.	C.G.	H.G.
21.3	99.6	42.1	At3g04000	819555	short-chain dehydrogenase/reductase (SDR) family protein	F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:unknown;BOMFPAV	O.I.	C.G.	H.G.
20.9	99.6	111.4	At4g27990	828912	YGGT family protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast, chloroplast envelope;BOP	O.I.	C.G.	H.G.
20.4	99.6	123.0	At3g54500	824615	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB	O.I.	C.G.	H.G.
20.2	99.6	51.0	At1g02100	837541	leucine carboxyl methyltransferase family protein	F:methyltransferase activity;P:biological_process unknown;C:cellular_component unknown;FMOP	O.I.	C.G.	H.G.
19.6	99.6	157.2	At5g54080	835494	HGO (HOMOGENTISATE 1,2-DIOXYGENASE)	homogentisate 1,2-dioxygenase	O.I.	C.G.	H.G.
19.4	99.6	49.8	At4g31080	829235	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPO	O.I.	C.G.	H.G.
19.3	99.6	114.7	At5g56140	835713	KH domain-containing protein	F:RNA binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPBOFVA	O.I.	C.G.	H.G.
19.3	99.6	88.0	At5g15850	831442	COL1 (constans-like 1)	Homologous to the flowering-time gene CONSTANS.	O.I.	C.G.	H.G.
19.2	99.6	33.4	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.
18.8	99.5	119.9	At3g03470	821250	CYP89A9	member of CYP89A	O.I.	C.G.	H.G.
18.7	99.5	71.2	At5g01240	831866	amino acid permease, putative	F:transporter activity;P:amino acid transport;C:membrane;PFMO	O.I.	C.G.	H.G.
18.7	99.5	54.2	At3g01560	821110	proline-rich family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBVA	O.I.	C.G.	H.G.
18.6	99.5	142.6	At1g07350	837246	transformer serine/arginine-rich ribonucleoprotein, putative	F:RNA binding, nucleotide binding, nucleic acid binding;P:RNA splicing;C:unknown;MPFOBVA	O.I.	C.G.	H.G.
18.5	99.5	87.3	At1g13380	837898	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
18.5	99.5	24.8	At3g11100	820281	transcription factor	F:transcription factor activity;P:regulation of transcription;C:nucleus;POMFBA	O.I.	C.G.	H.G.
18.4	99.5	182.7	At2g20920	816626	unknown protein	F:unknown;P:unknown;C:membrane;BPO	O.I.	C.G.	H.G.
18.2	99.5	100.5	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.
18.1	99.5	35.3	At1g01725	839271	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
18.0	99.5	56.8	At1g71480	843489	nuclear transport factor 2 (NTF2) family protein	F:protein transporter activity;P:transport, protein import into nucleus;C:chloroplast thylakoid membrane, nucleus, intracellular, chloroplast;PBO	O.I.	C.G.	H.G.
18.0	99.5	15.9	At1g75250	843862	ATRL6 (ARABIDOPSIS RAD-LIKE 6)	F:transcription factor activity;P:regulation of transcription;C:unknown;PMO	O.I.	C.G.	H.G.
17.6	99.5	124.0	At4g13830	827017	J20 (DNAJ-LIKE 20)	DnaJ-like protein (J20); nuclear gene	O.I.	C.G.	H.G.
17.5	99.5	80.3	At3g62190	825392	DNAJ heat shock N-terminal domain-containing protein	F:heat shock protein binding;P:protein folding;C:cellular_component unknown;OBMPFA	O.I.	C.G.	H.G.
17.5	99.5	45.4	At3g60080	825178	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.
17.1	99.5	49.1	At5g20380	832160	PHT4	Encodes an inorganic phosphate transporter (PHT4;5).	O.I.	C.G.	H.G.
17.1	99.5	15.4	At5g67190	836854	AP2 domain-containing transcription factor, putative	encodes a member of the DREB subfamily A-5 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 16 members in this subfamily including RAP2.1, RAP2.9 and RAP2.10.	O.I.	C.G.	H.G.
17.0	99.5	28.3	At3g01850	821068	ribulose-phosphate 3-epimerase, cytosolic, putative / pentose-5-phosphate 3-epimerase, putative	F:ribulose-phosphate 3-epimerase activity, catalytic activity;P:carbohydrate metabolic process, metabolic process;C:endomembrane system;OBMFPA	O.I.	C.G.	H.G.
16.9	99.5	34.7	At5g57360	835842	ZTL (ZEITLUPE)	Encodes clock-associated PAS protein ZTL; Also known as FKF1-like protein 2 or ADAGIO1(ADO1). A protein containing a PAS domain ZTL contributes to the plant fitness (carbon fixation, biomass) by influencing the circadian clock period. ZTL is the F-box component of an SCF complex implicated in the degradation of TOC1.	O.I.	C.G.	H.G.
16.9	99.5	26.3	At3g28080	822432	nodulin MtN21 family protein	F:molecular_function unknown;P:biological_process unknown;C:membrane;PBOAM	O.I.	C.G.	H.G.
16.8	99.5	47.6	At2g21950	816731	SKIP6 (SKP1 interacting partner 6)	Encodes an SKP1 interacting partner (SKIP6).	O.I.	C.G.	H.G.
16.6	99.5	46.9	At3g07870	819978	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	C.G.	H.G.
16.5	99.5	62.5	At4g26480	828754	KH domain-containing protein	F:nicotianamine synthase activity, RNA binding, nucleic acid binding;P:nicotianamine biosynthetic process;C:cellular_component unknown;MPFOB	O.I.	C.G.	H.G.
16.3	99.5	64.9	At1g80310	844371	sulfate transmembrane transporter	F:sulfate transmembrane transporter activity;P:response to salt stress;C:vacuole;BOPFMA	O.I.	C.G.	H.G.
15.9	99.5	39.7	At4g36780	829831	transcription regulator	F:transcription regulator activity;P:biological_process unknown;C:cellular_component unknown;PF	O.I.	C.G.	H.G.
15.8	99.5	54.8	At3g04350	819590	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFMBO	O.I.	C.G.	H.G.
15.6	99.5	60.2	At1g62960	842598	ACS10 (ACC SYNTHASE 10)	Encodes an aminotransferase with broad specificity for aspartate and aromatic amino aids such as tyrosine and phenylalanine. It does not act on branched chain amino acids and does not have ACC synthase activity.	O.I.	C.G.	H.G.
15.5	99.5	137.7	At3g07560	819945	PEX13 (PEROXIN 13)	Encodes peroxin 13 (PEX13) involved in protein transport into peroxisomes.	O.I.	C.G.	H.G.
15.5	99.5	69.8	At2g45620	819170	nucleotidyltransferase family protein	F:nucleotidyltransferase activity;P:biological_process unknown;C:cellular_component unknown;MOFPB	O.I.	C.G.	H.G.
15.5	99.5	57.0	At4g38860	830041	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	C.G.	H.G.
15.4	99.5	122.1	At1g19350	838518	BES1 (BRI1-EMS-SUPPRESSOR 1)	Encodes brassinosteroid (BR) signalling protein that accumulates in the nucleus as dephosphorylated form in response to BRs. Is phosphorylated by the BIN2 GSK3 kinase. It synergistically interacts with BIM1 to bind to E box sequences (CANNTG). The protein contains a nuclear localization signal (NLS), followed by a highly conserved amino-terminal domain (N) shared by all family members, a BIN2 phosphorylation domain (P), a PEST motif, involved in protein degradation in the absence of BR, and a carboxyl-terminal domain. BES1 can interact with the ELF6 and REF6 Jumonji N/C-domain containing proteins and may direct them to modify histone methylation upstream of some brassinosteroid responsive-genes	O.I.	C.G.	H.G.
15.4	99.5	57.1	At2g32530	817814	ATCSLB03	encodes a gene similar to cellulose synthase	O.I.	C.G.	H.G.
15.4	99.5	7.9	At2g35950	818168	EDA12 (embryo sac development arrest 12)	F:molecular_function unknown;P:megagametogenesis;C:unknown;P	O.I.	C.G.	H.G.
15.1	99.4	182.1	At2g34590	818024	transketolase family protein	F:pyruvate dehydrogenase (acetyl-transferring) activity, transketolase activity;P:pollen tube development;C:chloroplast, chloroplast envelope;BOMPFA	O.I.	C.G.	H.G.
15.0	99.4	219.6	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.
15.0	99.4	197.6	At1g58030	842170	CAT2 (CATIONIC AMINO ACID TRANSPORTER 2)	Encodes a member of the cationic amino acid transporter (CAT) subfamily of amino acid polyamine choline transporters. Localized to the tonoplast.	O.I.	C.G.	H.G.
14.9	99.4	59.1	At5g11840	831057	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;OBP	O.I.	C.G.	H.G.
14.9	99.4	30.9	At4g29820	829104	CFIM-25	Encodes a homolog of the protein CFI-25, a polyadenylation factor subunit.	O.I.	C.G.	H.G.
14.8	99.4	65.4	At1g08460	837366	HDA08	F:histone deacetylase activity;P:histone deacetylation;C:cellular_component unknown;OBMFPA	O.I.	C.G.	H.G.
14.7	99.4	38.0	At1g32520	840146	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;MPO	O.I.	C.G.	H.G.
14.7	99.4	25.0	At1g20890	838682	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PMO	O.I.	C.G.	H.G.
14.6	99.4	44.6	At4g17070	827415	peptidyl-prolyl cis-trans isomerase	F:peptidyl-prolyl cis-trans isomerase activity;P:response to oxidative stress;C:unknown;PBMO	O.I.	C.G.	H.G.
14.5	99.4	112.9	At3g55460	824712	SCL30	encodes an SC35-like splicing factor that is localized to nuclear specks.	O.I.	C.G.	H.G.
14.0	99.4	33.5	At5g05710	830455	pleckstrin homology (PH) domain-containing protein	F:molecular_function unknown;P:unknown;C:cellular_component unknown;MOPFV	O.I.	C.G.	H.G.
13.9	99.4	22.3	At1g48550	841276	vacuolar protein sorting-associated protein 26 family protein / VPS26 family protein	F:molecular_function unknown;P:intracellular protein transport, vacuolar transport, retrograde transport, endosome to Golgi;C:retromer complex;MOPF	O.I.	C.G.	H.G.
13.8	99.4	61.5	At2g47960	819408	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;MFOP	O.I.	C.G.	H.G.
13.8	99.4	11.6	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.
13.7	99.4	217.4	At5g16110	831468	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
13.7	99.4	41.4	At2g23760	816908	BLH4 (BEL1-LIKE HOMEODOMAIN 4)	Encodes a member of the BEL family of homeodomain proteins. Plants doubly mutant for saw1/saw2 (blh2/blh4) have serrated leaves. BP is expressed in the serrated leaves, therefore saw2 and saw1 may act redundantly to repress BP in leaves.	O.I.	C.G.	H.G.
13.7	99.4	26.5	At5g51170	835191	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPO	O.I.	C.G.	H.G.
13.6	99.4	201.2	At2g39570	818542	ACT domain-containing protein	F:amino acid binding;P:metabolic process;C:unknown;POB	O.I.	C.G.	H.G.
13.6	99.4	96.9	At5g22000	832260	RHF2A (RING-H2 GROUP F2A)	encodes a RING-type E3 ubiquitin ligase implicated in gametogenesis. Double mutant analyses with RHF1a suggests that RHF2a may be involved in targetting ICK4KRP6 for degradation following meiosis in order to allow the mitoses associated with megagametogenesis and microgametogenesis to occur. RHF2a is expressed in all four floral whorls and is present at ~8-fold higher levels than RHF1a in inflorescences by RT-PCR analyses.	O.I.	C.G.	H.G.
13.6	99.4	38.8	At2g21195	816656	unknown protein	F:molecular_function unknown;P:response to oxidative stress;C:cellular_component unknown;P	O.I.	C.G.	H.G.
13.6	99.4	27.2	At1g51360	841560	DABB1 (DIMERIC A/B BARREL DOMAINS-PROTEIN 1)	Involved in defense against fungal pathogens and located in cytosol.	O.I.	C.G.	H.G.
13.4	99.4	44.7	At2g33250	817887	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
13.3	99.4	75.1	At2g21185	816654	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	C.G.	H.G.
13.3	99.4	47.4	At5g59080	836025	unknown protein	F:molecular_function unknown;P:response to oxidative stress;C:chloroplast;P	O.I.	C.G.	H.G.
13.1	99.4	45.8	At5g50520	835120	nodulin family protein	F:unknown;P:unknown;C:endomembrane system;BOPFMA	O.I.	C.G.	H.G.
13.1	99.4	42.7	At1g64500	842758	glutaredoxin family protein	F:electron carrier activity, protein disulfide oxidoreductase activity;P:N-terminal protein myristoylation, cell redox homeostasis;C:cellular_component unknown;PMBOF	O.I.	C.G.	H.G.
13.1	99.4	39.1	At1g19680	838555	protein binding / zinc ion binding	F:protein binding, zinc ion binding;P:N-terminal protein myristoylation;C:unknown;OPMBF	O.I.	C.G.	H.G.
12.9	99.3	94.4	At5g32440	833203	-	F:unknown;P:unknown;C:chloroplast;OPMFB	O.I.	C.G.	H.G.
12.9	99.3	33.8	At1g33250	840219	fringe-related protein	F:transferase activity, transferring glycosyl groups;P:unknown;C:chloroplast, membrane;MPFO	O.I.	C.G.	H.G.
12.8	99.3	129.3	At1g29970	839876	RPL18AA (60S RIBOSOMAL PROTEIN L18A-1)	F:unknown;P:unknown;C:unknown;P	O.I.	C.G.	H.G.

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GSM ID	GSM128650
Assay name	Underwood_1-3_Cor-10e6-24h_Rep3_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 GSM128650 Assay name Underwood_1-3_Cor-10e6-24h_Rep3_ATH1 GSE experiment GSE5520: Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction

GSM ID GSM128650

Assay name Underwood_1-3_Cor-10e6-24h_Rep3_ATH1

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