CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM134518

Assay name Col-0_4day_red illumination_-lincomycin_rep2

GSE experiment GSE5759: red illumination w/o lincomycin

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
99.7 99.9 214.8 At5g15290 831381 integral membrane family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
59.8 99.8 193.3 At5g02020 831782 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
52.9 99.8 146.7 At4g16515 827350 unknown protein F:molecular_function unknown;P:unknown;C:endomembrane system;P O.I. C.G. H.G.
50.2 99.8 73.2 At5g04770 830355 CAT6 (CATIONIC AMINO ACID TRANSPORTER 6) Encodes a member of the cationic amino acid transporter (CAT) subfamily of amino acid polyamine choline transporters. Does not mediate efficient uptake of basic amino acids in yeast or Xenopus systems but can transport neutral and acidic amino acid analogs. Expressed in sink tissues. Induced during infestation of roots by the plant parasitic root-knot nematode, Meloidogyne incognita. Localized in the plasma membrane. O.I. C.G. H.G.
40.7 99.8 64.8 At4g22460 828341 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein F:lipid binding;P:lipid transport;C:endomembrane system;P O.I. C.G. H.G.
39.9 99.8 93.9 At1g64640 842772 plastocyanin-like domain-containing protein F:electron carrier activity, copper ion binding;P:unknown;C:anchored to membrane;P O.I. C.G. H.G.
39.5 99.8 112.7 At4g25260 828629 invertase/pectin methylesterase inhibitor family protein F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:shade avoidance;C:endomembrane system;P O.I. C.G. H.G.
37.5 99.7 289.2 At5g53250 835406 AGP22 (ARABINOGALACTAN PROTEIN 22) F:unknown;P:unknown;C:anchored to membrane;P O.I. C.G. H.G.
37.2 99.7 66.4 At3g05150 819677 sugar transporter family protein F:carbohydrate transmembrane transporter activity, sugar:hydrogen symporter activity;P:transport, transmembrane transport;C:nucleus, membrane;BMFPOA O.I. C.G. H.G.
36.7 99.7 252.5 At5g60660 836187 PIP2 F:water channel activity;P:transport;C:integral to membrane, membrane;BPMOFAV O.I. C.G. H.G.
36.5 99.7 311.9 At5g65390 836664 AGP7 F:unknown;P:unknown;C:anchored to membrane;BMOPFVA O.I. C.G. H.G.
35.9 99.7 129.1 At5g54190 835507 PORA light-dependent NADPH:protochlorophyllide oxidoreductase A O.I. C.G. H.G.
34.9 99.7 24.1 At1g52250 - - O.I. C.G. H.G.
34.7 99.7 94.3 At5g44920 834522 Toll-Interleukin-Resistance (TIR) domain-containing protein F:transmembrane receptor activity;P:signal transduction, defense response, innate immune response;C:endoplasmic reticulum;PBO O.I. C.G. H.G.
34.1 99.7 116.8 At1g20190 838608 ATEXPA11 (ARABIDOPSIS THALIANA EXPANSIN 11) member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio) O.I. C.G. H.G.
32.9 99.7 207.8 At3g13720 820581 PRA8 F:molecular_function unknown;P:vesicle-mediated transport;C:endoplasmic reticulum;POMF O.I. C.G. H.G.
32.5 99.7 161.7 At1g30750 839955 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;OBMFPV O.I. C.G. H.G.
32.0 99.7 111.0 At3g48970 824058 copper-binding family protein F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:unknown;PBO O.I. C.G. H.G.
30.3 99.7 81.2 At1g08500 837371 plastocyanin-like domain-containing protein F:electron carrier activity, copper ion binding;P:unknown;C:anchored to membrane;P O.I. C.G. H.G.
30.2 99.7 49.2 At5g52250 835301 transducin family protein / WD-40 repeat family protein Encodes a transducin protein whose gene expression is induced by UV-B. This induction is reduced in hy5 mutant and may be a target of HY5 during UV-B response. O.I. C.G. H.G.
30.0 99.7 280.2 At5g10430 830907 AGP4 (ARABINOGALACTAN PROTEIN 4) Encodes arabinogalactan-protein (AGP4). O.I. C.G. H.G.
28.8 99.7 63.3 At1g22740 838880 RABG3B GTP-binding protein Rab7 O.I. C.G. H.G.
28.3 99.7 118.8 At1g67910 843119 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
27.5 99.7 215.4 At1g32170 840109 XTR4 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 4) xyloglucan endotransglycosylase-related protein (XTR4) O.I. C.G. H.G.
27.0 99.7 86.3 At3g17100 820967 transcription factor F:transcription factor activity;P:regulation of transcription;C:nucleus, chloroplast;PM O.I. C.G. H.G.
26.9 99.7 202.1 At1g25230 839105 purple acid phosphatase family protein F:hydrolase activity, protein serine/threonine phosphatase activity;P:biological_process unknown;C:endomembrane system;MOBPF O.I. C.G. H.G.
26.5 99.7 97.0 At1g61900 842486 unknown protein F:molecular_function unknown;P:biological_process unknown;C:anchored to plasma membrane, plasma membrane, anchored to membrane;P O.I. C.G. H.G.
26.0 99.7 73.7 At5g07110 830602 PRA1.B6 (PRENYLATED RAB ACCEPTOR 1.B6) F:molecular_function unknown;P:vesicle-mediated transport;C:endoplasmic reticulum;PMFO O.I. C.G. H.G.
25.2 99.6 172.0 At4g11360 826738 RHA1B Encodes a putative RING-H2 finger protein RHA1b. O.I. C.G. H.G.
25.2 99.6 29.8 At1g72070 843538 DNAJ heat shock N-terminal domain-containing protein F:unfolded protein binding, heat shock protein binding;P:protein folding;C:unknown;BOMPFAV O.I. C.G. H.G.
24.9 99.6 9.6 At3g03830 821123 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. C.G. H.G.
23.9 99.6 157.9 At1g12080 837760 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA O.I. C.G. H.G.
23.9 99.6 50.8 At3g23880 821971 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:nucleus;PO O.I. C.G. H.G.
23.8 99.6 54.9 At3g05920 819761 heavy-metal-associated domain-containing protein F:metal ion binding;P:metal ion transport;C:cellular_component unknown;PMOBVFA O.I. C.G. H.G.
23.4 99.6 28.4 At2g36080 818181 DNA-binding protein, putative Encodes a plant-specific B3 DNA-binding domain transcription factor. Has transcription repressor activity. O.I. C.G. H.G.
22.9 99.6 16.1 At4g23030 828402 MATE efflux protein-related F:antiporter activity, drug transporter activity, transporter activity;P:multidrug transport;C:membrane;BOPFAM O.I. C.G. H.G.
22.8 99.6 241.7 At5g47450 834794 AtTIP2 Tonoplast intrinsic protein, transports ammonium (NH3) and methylammonium across the tonoplast membrane, gene expression shows diurnal regulation and is upregulated by ammonium (NH3). O.I. C.G. H.G.
22.2 99.6 16.5 At2g19660 816485 DC1 domain-containing protein F:molecular_function unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMO O.I. C.G. H.G.
22.2 99.6 9.8 At2g18010 816313 auxin-responsive family protein F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. C.G. H.G.
21.6 99.6 218.3 At2g21140 816649 ATPRP2 (PROLINE-RICH PROTEIN 2) Proline-rich protein expressed in expanding leaves, stems, flowers, and siliques. O.I. C.G. H.G.
21.6 99.6 89.8 At4g25830 828688 integral membrane family protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
21.6 99.6 30.5 At3g52480 824413 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
21.4 99.6 312.7 At5g09440 830803 EXL4 (EXORDIUM LIKE 4) F:molecular_function unknown;P:biological_process unknown;C:membrane;PB O.I. C.G. H.G.
21.3 99.6 98.9 At1g11545 837698 xyloglucan:xyloglucosyl transferase, putative / xyloglucan endotransglycosylase, putative / endo-xyloglucan transferase, putative F:hydrolase activity, acting on glycosyl bonds, xyloglucan:xyloglucosyl transferase activity, hydrolase activity, hydrolyzing O-glycosyl compounds;P:carbohydrate metabolic process, cellular glucan metabolic process;C:endomembrane system, cell wall, apoplast;PFBO O.I. C.G. H.G.
21.3 99.6 19.4 At1g06980 837208 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
20.9 99.6 24.1 At1g17700 838346 PRA1.F1 (PRENYLATED RAB ACCEPTOR 1.F1) F:molecular_function unknown;P:vesicle-mediated transport;C:endoplasmic reticulum;PMOF O.I. C.G. H.G.
20.8 99.6 49.5 At5g06200 830507 integral membrane family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
20.7 99.6 210.2 At2g43535 818955 trypsin inhibitor, putative Encodes a defensin-like (DEFL) family protein. O.I. C.G. H.G.
20.7 99.6 27.6 At2g26710 817212 BAS1 (PHYB ACTIVATION TAGGED SUPPRESSOR 1) Encodes a member of the cytochrome p450 family that serves as a control point between multiple photoreceptor systems and brassinosteroid signal transduction. Involved in brassinolide metabolism. Mediates response to a variety of light signals including hypocotyl elongation and cotyledon expansion. O.I. C.G. H.G.
20.6 99.6 236.8 At4g32460 829381 - F:molecular_function unknown;P:biological_process unknown;C:plant-type cell wall;PB O.I. C.G. H.G.
20.2 99.6 119.6 At1g70710 843408 ATGH9B1 (ARABIDOPSIS THALIANA GLYCOSYL HYDROLASE 9B1) endo-1,4-beta-glucanase. Involved in cell elongation. O.I. C.G. H.G.
20.0 99.6 277.1 At4g14130 827051 XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7) xyloglucan endotransglycosylase-related protein (XTR7) O.I. C.G. H.G.
20.0 99.6 175.2 At2g28670 817416 disease resistance-responsive family protein / fibroin-related F:molecular_function unknown;P:unknown;C:endomembrane system;BMOPFVA O.I. C.G. H.G.
20.0 99.6 34.4 At4g11610 826766 C2 domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOF O.I. C.G. H.G.
19.9 99.6 80.3 At1g15350 838104 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PO O.I. C.G. H.G.
19.8 99.6 179.4 At2g43050 818907 ATPMEPCRD F:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:cell wall, plant-type cell wall;PBFM O.I. C.G. H.G.
19.8 99.6 64.5 At3g50660 824229 DWF4 (DWARF 4) Encodes a 22α hydroxylase whose reaction is a rate-limiting step in brassinosteroid biosynthetic pathway. The protein is a member of CYP90B gene family. CLM is an epi-allele with small, compressed rosette, reduced internode length, and reduced fertility, appears in selfed ddm mutant plants possibly due to loss of cytosine methylation. Transcripts accumulate in actively growing tissues, and GUS expression is negatively regulated by brassinosteroids. Localized in the endoplasmic reticulum. The in vitro expressed protein can perform the C-22 hydroxylation of a variety of C27-, C28- and C29-sterols. Cholesterol was the best substrate, followed by campesterol. Sitosterol was a poor substrate. O.I. C.G. H.G.
19.7 99.6 90.7 At4g28050 828920 TET7 (TETRASPANIN7) Member of TETRASPANIN family O.I. C.G. H.G.
19.3 99.6 160.3 At3g60140 825184 DIN2 (DARK INDUCIBLE 2) Encodes a protein similar to beta-glucosidase and is a member of glycoside hydrolase family 1. Expression is induced after 24 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell. O.I. C.G. H.G.
19.1 99.6 152.5 At1g09570 837483 PHYA (PHYTOCHROME A) Light-labile cytoplasmic red/far-red light photoreceptor involved in the regulation of photomorphogenesis. It exists in two inter-convertible forms: Pr and Pfr (active) and functions as a dimer.The N terminus carries a single tetrapyrrole chromophore, and the C terminus is involved in dimerization. It is the sole photoreceptor mediating the FR high irradiance response (HIR). Major regulator in red-light induction of phototropic enhancement. Involved in the regulation of de-etiolation. Involved in gravitropism and phototropism. Requires FHY1 for nuclear accumulation. O.I. C.G. H.G.
19.0 99.5 18.5 At4g01140 828157 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO O.I. C.G. H.G.
18.8 99.5 26.9 At4g01410 828166 harpin-induced family protein / HIN1 family protein / harpin-responsive family protein F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;P O.I. C.G. H.G.
18.5 99.5 91.2 At4g11190 826721 disease resistance-responsive family protein / dirigent family protein F:molecular_function unknown;P:lignan biosynthetic process, defense response;C:endomembrane system;P O.I. C.G. H.G.
18.5 99.5 54.3 At1g72200 843552 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVB O.I. C.G. H.G.
18.0 99.5 65.6 At1g62770 842576 invertase/pectin methylesterase inhibitor family protein F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
17.9 99.5 360.7 At2g05540 815103 glycine-rich protein F:unknown;P:unknown;C:endomembrane system;MPBOFVA O.I. C.G. H.G.
17.9 99.5 220.3 At1g28330 839729 DYL1 (DORMANCY-ASSOCIATED PROTEIN-LIKE 1) dormancy-associated protein (DRM1) O.I. C.G. H.G.
17.7 99.5 378.0 At1g03870 839384 FLA9 (FASCICLIN-LIKE ARABINOOGALACTAN 9) fasciclin-like arabinogalactan-protein 9 (Fla9) O.I. C.G. H.G.
17.7 99.5 30.1 At4g00560 827978 methionine adenosyltransferase regulatory beta subunit-related F:dTDP-4-dehydrorhamnose reductase activity, binding, catalytic activity;P:dTDP-rhamnose biosynthetic process, extracellular polysaccharide biosynthetic process, metabolic process;C:endomembrane system;BOAMFP O.I. C.G. H.G.
17.6 99.5 108.3 At5g43580 834378 serine-type endopeptidase inhibitor Predicted to encode a PR (pathogenesis-related) peptide that belongs to the PR-6 proteinase inhibitor family. Six putative PR-6-type protein encoding genes are found in Arabidopsis: At2g38900, At2g38870, At5g43570, At5g43580, At3g50020 and At3g46860. O.I. C.G. H.G.
17.6 99.5 101.9 At5g26740 832714 unknown protein F:unknown;P:unknown;C:endomembrane system;MPFO O.I. C.G. H.G.
17.4 99.5 63.8 At2g40420 818635 amino acid transporter family protein Encodes a putative amino acid transporter. O.I. C.G. H.G.
17.4 99.5 17.2 At1g43590 840943 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
17.3 99.5 107.6 At2g37640 818341 EXP3 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.
17.2 99.5 93.7 At5g04470 830326 SIM (SIAMESE) Encodes a novel nuclear 14-kD protein containing a cyclin binding motif and a motif found in ICK/KRP cell cycle inhibitor proteins. It is required for coordinating cell division and cell differentiation during the development of Arabidopsis trichomes, playing a key role in the mitosis-to-endoreduplication transition. It interacts with D-type cyclins in vivo. O.I. C.G. H.G.
17.2 99.5 40.7 At5g24170 832484 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFP O.I. C.G. H.G.
16.9 99.5 222.9 At3g12610 820441 DRT100 (DNA-DAMAGE REPAIR/TOLERATION 100) Plays role in DNA-damage repair/toleration. Partially complements RecA- phenotypes. O.I. C.G. H.G.
16.7 99.5 61.2 At2g27370 817280 integral membrane family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
16.6 99.5 265.3 At4g21850 828273 methionine sulfoxide reductase domain-containing protein / SeIR domain-containing protein F:peptide-methionine-(S)-S-oxide reductase activity;P:biological_process unknown;C:cellular_component unknown;OBMPFAV O.I. C.G. H.G.
16.5 99.5 48.2 At3g62860 825461 esterase/lipase/thioesterase family protein F:catalytic activity;P:unknown;C:plasma membrane;BOPMFVA O.I. C.G. H.G.
16.4 99.5 121.0 At4g18970 827632 GDSL-motif lipase/hydrolase family protein F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBFOM O.I. C.G. H.G.
16.1 99.5 102.2 At2g34070 817968 unknown protein F:unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
15.9 99.5 103.5 At1g75900 843923 family II extracellular lipase 3 (EXL3) F:lipase activity, carboxylesterase activity, acyltransferase activity;P:sexual reproduction;C:extracellular region;PBFOM O.I. C.G. H.G.
15.9 99.5 62.9 At2g47930 819405 AGP26 (ARABINOGALACTAN PROTEIN 26) F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;OPMVBFA O.I. C.G. H.G.
15.9 99.5 13.0 At1g27670 839659 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
15.7 99.5 58.0 At3g60530 825224 zinc finger (GATA type) family protein F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;PFOM O.I. C.G. H.G.
15.4 99.5 104.6 At5g22500 832311 FAR1 (FATTY ACID REDUCTASE 1) F:oxidoreductase activity, acting on the CH-CH group of donors, fatty acyl-CoA reductase (alcohol-forming) activity;P:microsporogenesis, metabolic process;C:chloroplast;MBFOP O.I. C.G. H.G.
15.4 99.5 32.7 At4g23870 828486 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
15.2 99.4 115.7 At4g20870 827835 FAH2 (FATTY ACID HYDROXYLASE 2) encodes a fatty acid hydroxylase, required for the AtBI-1-mediated suppression of programmed cell death. O.I. C.G. H.G.
15.2 99.4 62.5 At2g32690 3768391 GRP23 (GLYCINE-RICH PROTEIN 23) Glycine-rich protein similar in structure to GRP5. The expression of GRP23 is induced by HPA (cutin monomer, salicylic acid, and abscisic acid. O.I. C.G. H.G.
15.0 99.4 142.8 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.
14.9 99.4 172.5 At1g22530 838859 PATL2 (PATELLIN 2) F:transporter activity;P:transport;C:plasma membrane, chloroplast;MOBFPVA O.I. C.G. H.G.
14.9 99.4 47.4 At3g57790 824949 glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein F:polygalacturonase activity;P:carbohydrate metabolic process;C:plasma membrane;PBFOMAV O.I. C.G. H.G.
14.8 99.4 14.1 At2g22890 816820 small conjugating protein ligase F:small conjugating protein ligase activity;P:regulation of protein metabolic process, post-translational protein modification;C:chloroplast;MOPBV O.I. C.G. H.G.
14.6 99.4 305.2 At2g37130 818289 peroxidase 21 (PER21) (P21) (PRXR5) F:electron carrier activity, peroxidase activity, heme binding;P:defense response to fungus;C:endomembrane system;PFO O.I. C.G. H.G.
14.5 99.4 196.7 At2g36100 818183 integral membrane family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
14.5 99.4 116.9 At5g24570 832528 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. C.G. H.G.
14.5 99.4 65.6 At5g41080 834110 glycerophosphoryl diester phosphodiesterase family protein F:phosphoric diester hydrolase activity, glycerophosphodiester phosphodiesterase activity;P:glycerol metabolic process, lipid metabolic process;C:unknown;BOMFPAV O.I. C.G. H.G.
14.4 99.4 348.0 At3g21720 821726 ICL (ISOCITRATE LYASE) Encodes a glyoxylate cycle enzyme isocitrate lyase (ICL). O.I. C.G. H.G.
14.4 99.4 27.4 At2g42900 818891 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM 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.
99.7	99.9	214.8	At5g15290	831381	integral membrane family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
59.8	99.8	193.3	At5g02020	831782	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
52.9	99.8	146.7	At4g16515	827350	unknown protein	F:molecular_function unknown;P:unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
50.2	99.8	73.2	At5g04770	830355	CAT6 (CATIONIC AMINO ACID TRANSPORTER 6)	Encodes a member of the cationic amino acid transporter (CAT) subfamily of amino acid polyamine choline transporters. Does not mediate efficient uptake of basic amino acids in yeast or Xenopus systems but can transport neutral and acidic amino acid analogs. Expressed in sink tissues. Induced during infestation of roots by the plant parasitic root-knot nematode, Meloidogyne incognita. Localized in the plasma membrane.	O.I.	C.G.	H.G.
40.7	99.8	64.8	At4g22460	828341	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	F:lipid binding;P:lipid transport;C:endomembrane system;P	O.I.	C.G.	H.G.
39.9	99.8	93.9	At1g64640	842772	plastocyanin-like domain-containing protein	F:electron carrier activity, copper ion binding;P:unknown;C:anchored to membrane;P	O.I.	C.G.	H.G.
39.5	99.8	112.7	At4g25260	828629	invertase/pectin methylesterase inhibitor family protein	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:shade avoidance;C:endomembrane system;P	O.I.	C.G.	H.G.
37.5	99.7	289.2	At5g53250	835406	AGP22 (ARABINOGALACTAN PROTEIN 22)	F:unknown;P:unknown;C:anchored to membrane;P	O.I.	C.G.	H.G.
37.2	99.7	66.4	At3g05150	819677	sugar transporter family protein	F:carbohydrate transmembrane transporter activity, sugar:hydrogen symporter activity;P:transport, transmembrane transport;C:nucleus, membrane;BMFPOA	O.I.	C.G.	H.G.
36.7	99.7	252.5	At5g60660	836187	PIP2	F:water channel activity;P:transport;C:integral to membrane, membrane;BPMOFAV	O.I.	C.G.	H.G.
36.5	99.7	311.9	At5g65390	836664	AGP7	F:unknown;P:unknown;C:anchored to membrane;BMOPFVA	O.I.	C.G.	H.G.
35.9	99.7	129.1	At5g54190	835507	PORA	light-dependent NADPH:protochlorophyllide oxidoreductase A	O.I.	C.G.	H.G.
34.9	99.7	24.1	At1g52250		-	-	O.I.	C.G.	H.G.
34.7	99.7	94.3	At5g44920	834522	Toll-Interleukin-Resistance (TIR) domain-containing protein	F:transmembrane receptor activity;P:signal transduction, defense response, innate immune response;C:endoplasmic reticulum;PBO	O.I.	C.G.	H.G.
34.1	99.7	116.8	At1g20190	838608	ATEXPA11 (ARABIDOPSIS THALIANA EXPANSIN 11)	member of Alpha-Expansin Gene Family. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio)	O.I.	C.G.	H.G.
32.9	99.7	207.8	At3g13720	820581	PRA8	F:molecular_function unknown;P:vesicle-mediated transport;C:endoplasmic reticulum;POMF	O.I.	C.G.	H.G.
32.5	99.7	161.7	At1g30750	839955	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;OBMFPV	O.I.	C.G.	H.G.
32.0	99.7	111.0	At3g48970	824058	copper-binding family protein	F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:unknown;PBO	O.I.	C.G.	H.G.
30.3	99.7	81.2	At1g08500	837371	plastocyanin-like domain-containing protein	F:electron carrier activity, copper ion binding;P:unknown;C:anchored to membrane;P	O.I.	C.G.	H.G.
30.2	99.7	49.2	At5g52250	835301	transducin family protein / WD-40 repeat family protein	Encodes a transducin protein whose gene expression is induced by UV-B. This induction is reduced in hy5 mutant and may be a target of HY5 during UV-B response.	O.I.	C.G.	H.G.
30.0	99.7	280.2	At5g10430	830907	AGP4 (ARABINOGALACTAN PROTEIN 4)	Encodes arabinogalactan-protein (AGP4).	O.I.	C.G.	H.G.
28.8	99.7	63.3	At1g22740	838880	RABG3B	GTP-binding protein Rab7	O.I.	C.G.	H.G.
28.3	99.7	118.8	At1g67910	843119	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
27.5	99.7	215.4	At1g32170	840109	XTR4 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 4)	xyloglucan endotransglycosylase-related protein (XTR4)	O.I.	C.G.	H.G.
27.0	99.7	86.3	At3g17100	820967	transcription factor	F:transcription factor activity;P:regulation of transcription;C:nucleus, chloroplast;PM	O.I.	C.G.	H.G.
26.9	99.7	202.1	At1g25230	839105	purple acid phosphatase family protein	F:hydrolase activity, protein serine/threonine phosphatase activity;P:biological_process unknown;C:endomembrane system;MOBPF	O.I.	C.G.	H.G.
26.5	99.7	97.0	At1g61900	842486	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:anchored to plasma membrane, plasma membrane, anchored to membrane;P	O.I.	C.G.	H.G.
26.0	99.7	73.7	At5g07110	830602	PRA1.B6 (PRENYLATED RAB ACCEPTOR 1.B6)	F:molecular_function unknown;P:vesicle-mediated transport;C:endoplasmic reticulum;PMFO	O.I.	C.G.	H.G.
25.2	99.6	172.0	At4g11360	826738	RHA1B	Encodes a putative RING-H2 finger protein RHA1b.	O.I.	C.G.	H.G.
25.2	99.6	29.8	At1g72070	843538	DNAJ heat shock N-terminal domain-containing protein	F:unfolded protein binding, heat shock protein binding;P:protein folding;C:unknown;BOMPFAV	O.I.	C.G.	H.G.
24.9	99.6	9.6	At3g03830	821123	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	C.G.	H.G.
23.9	99.6	157.9	At1g12080	837760	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA	O.I.	C.G.	H.G.
23.9	99.6	50.8	At3g23880	821971	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:nucleus;PO	O.I.	C.G.	H.G.
23.8	99.6	54.9	At3g05920	819761	heavy-metal-associated domain-containing protein	F:metal ion binding;P:metal ion transport;C:cellular_component unknown;PMOBVFA	O.I.	C.G.	H.G.
23.4	99.6	28.4	At2g36080	818181	DNA-binding protein, putative	Encodes a plant-specific B3 DNA-binding domain transcription factor. Has transcription repressor activity.	O.I.	C.G.	H.G.
22.9	99.6	16.1	At4g23030	828402	MATE efflux protein-related	F:antiporter activity, drug transporter activity, transporter activity;P:multidrug transport;C:membrane;BOPFAM	O.I.	C.G.	H.G.
22.8	99.6	241.7	At5g47450	834794	AtTIP2	Tonoplast intrinsic protein, transports ammonium (NH3) and methylammonium across the tonoplast membrane, gene expression shows diurnal regulation and is upregulated by ammonium (NH3).	O.I.	C.G.	H.G.
22.2	99.6	16.5	At2g19660	816485	DC1 domain-containing protein	F:molecular_function unknown;P:intracellular signaling cascade;C:cellular_component unknown;PMO	O.I.	C.G.	H.G.
22.2	99.6	9.8	At2g18010	816313	auxin-responsive family protein	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	C.G.	H.G.
21.6	99.6	218.3	At2g21140	816649	ATPRP2 (PROLINE-RICH PROTEIN 2)	Proline-rich protein expressed in expanding leaves, stems, flowers, and siliques.	O.I.	C.G.	H.G.
21.6	99.6	89.8	At4g25830	828688	integral membrane family protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
21.6	99.6	30.5	At3g52480	824413	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
21.4	99.6	312.7	At5g09440	830803	EXL4 (EXORDIUM LIKE 4)	F:molecular_function unknown;P:biological_process unknown;C:membrane;PB	O.I.	C.G.	H.G.
21.3	99.6	98.9	At1g11545	837698	xyloglucan:xyloglucosyl transferase, putative / xyloglucan endotransglycosylase, putative / endo-xyloglucan transferase, putative	F:hydrolase activity, acting on glycosyl bonds, xyloglucan:xyloglucosyl transferase activity, hydrolase activity, hydrolyzing O-glycosyl compounds;P:carbohydrate metabolic process, cellular glucan metabolic process;C:endomembrane system, cell wall, apoplast;PFBO	O.I.	C.G.	H.G.
21.3	99.6	19.4	At1g06980	837208	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
20.9	99.6	24.1	At1g17700	838346	PRA1.F1 (PRENYLATED RAB ACCEPTOR 1.F1)	F:molecular_function unknown;P:vesicle-mediated transport;C:endoplasmic reticulum;PMOF	O.I.	C.G.	H.G.
20.8	99.6	49.5	At5g06200	830507	integral membrane family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
20.7	99.6	210.2	At2g43535	818955	trypsin inhibitor, putative	Encodes a defensin-like (DEFL) family protein.	O.I.	C.G.	H.G.
20.7	99.6	27.6	At2g26710	817212	BAS1 (PHYB ACTIVATION TAGGED SUPPRESSOR 1)	Encodes a member of the cytochrome p450 family that serves as a control point between multiple photoreceptor systems and brassinosteroid signal transduction. Involved in brassinolide metabolism. Mediates response to a variety of light signals including hypocotyl elongation and cotyledon expansion.	O.I.	C.G.	H.G.
20.6	99.6	236.8	At4g32460	829381	-	F:molecular_function unknown;P:biological_process unknown;C:plant-type cell wall;PB	O.I.	C.G.	H.G.
20.2	99.6	119.6	At1g70710	843408	ATGH9B1 (ARABIDOPSIS THALIANA GLYCOSYL HYDROLASE 9B1)	endo-1,4-beta-glucanase. Involved in cell elongation.	O.I.	C.G.	H.G.
20.0	99.6	277.1	At4g14130	827051	XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7)	xyloglucan endotransglycosylase-related protein (XTR7)	O.I.	C.G.	H.G.
20.0	99.6	175.2	At2g28670	817416	disease resistance-responsive family protein / fibroin-related	F:molecular_function unknown;P:unknown;C:endomembrane system;BMOPFVA	O.I.	C.G.	H.G.
20.0	99.6	34.4	At4g11610	826766	C2 domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOF	O.I.	C.G.	H.G.
19.9	99.6	80.3	At1g15350	838104	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PO	O.I.	C.G.	H.G.
19.8	99.6	179.4	At2g43050	818907	ATPMEPCRD	F:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:cell wall, plant-type cell wall;PBFM	O.I.	C.G.	H.G.
19.8	99.6	64.5	At3g50660	824229	DWF4 (DWARF 4)	Encodes a 22α hydroxylase whose reaction is a rate-limiting step in brassinosteroid biosynthetic pathway. The protein is a member of CYP90B gene family. CLM is an epi-allele with small, compressed rosette, reduced internode length, and reduced fertility, appears in selfed ddm mutant plants possibly due to loss of cytosine methylation. Transcripts accumulate in actively growing tissues, and GUS expression is negatively regulated by brassinosteroids. Localized in the endoplasmic reticulum. The in vitro expressed protein can perform the C-22 hydroxylation of a variety of C27-, C28- and C29-sterols. Cholesterol was the best substrate, followed by campesterol. Sitosterol was a poor substrate.	O.I.	C.G.	H.G.
19.7	99.6	90.7	At4g28050	828920	TET7 (TETRASPANIN7)	Member of TETRASPANIN family	O.I.	C.G.	H.G.
19.3	99.6	160.3	At3g60140	825184	DIN2 (DARK INDUCIBLE 2)	Encodes a protein similar to beta-glucosidase and is a member of glycoside hydrolase family 1. Expression is induced after 24 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell.	O.I.	C.G.	H.G.
19.1	99.6	152.5	At1g09570	837483	PHYA (PHYTOCHROME A)	Light-labile cytoplasmic red/far-red light photoreceptor involved in the regulation of photomorphogenesis. It exists in two inter-convertible forms: Pr and Pfr (active) and functions as a dimer.The N terminus carries a single tetrapyrrole chromophore, and the C terminus is involved in dimerization. It is the sole photoreceptor mediating the FR high irradiance response (HIR). Major regulator in red-light induction of phototropic enhancement. Involved in the regulation of de-etiolation. Involved in gravitropism and phototropism. Requires FHY1 for nuclear accumulation.	O.I.	C.G.	H.G.
19.0	99.5	18.5	At4g01140	828157	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO	O.I.	C.G.	H.G.
18.8	99.5	26.9	At4g01410	828166	harpin-induced family protein / HIN1 family protein / harpin-responsive family protein	F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;P	O.I.	C.G.	H.G.
18.5	99.5	91.2	At4g11190	826721	disease resistance-responsive family protein / dirigent family protein	F:molecular_function unknown;P:lignan biosynthetic process, defense response;C:endomembrane system;P	O.I.	C.G.	H.G.
18.5	99.5	54.3	At1g72200	843552	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVB	O.I.	C.G.	H.G.
18.0	99.5	65.6	At1g62770	842576	invertase/pectin methylesterase inhibitor family protein	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
17.9	99.5	360.7	At2g05540	815103	glycine-rich protein	F:unknown;P:unknown;C:endomembrane system;MPBOFVA	O.I.	C.G.	H.G.
17.9	99.5	220.3	At1g28330	839729	DYL1 (DORMANCY-ASSOCIATED PROTEIN-LIKE 1)	dormancy-associated protein (DRM1)	O.I.	C.G.	H.G.
17.7	99.5	378.0	At1g03870	839384	FLA9 (FASCICLIN-LIKE ARABINOOGALACTAN 9)	fasciclin-like arabinogalactan-protein 9 (Fla9)	O.I.	C.G.	H.G.
17.7	99.5	30.1	At4g00560	827978	methionine adenosyltransferase regulatory beta subunit-related	F:dTDP-4-dehydrorhamnose reductase activity, binding, catalytic activity;P:dTDP-rhamnose biosynthetic process, extracellular polysaccharide biosynthetic process, metabolic process;C:endomembrane system;BOAMFP	O.I.	C.G.	H.G.
17.6	99.5	108.3	At5g43580	834378	serine-type endopeptidase inhibitor	Predicted to encode a PR (pathogenesis-related) peptide that belongs to the PR-6 proteinase inhibitor family. Six putative PR-6-type protein encoding genes are found in Arabidopsis: At2g38900, At2g38870, At5g43570, At5g43580, At3g50020 and At3g46860.	O.I.	C.G.	H.G.
17.6	99.5	101.9	At5g26740	832714	unknown protein	F:unknown;P:unknown;C:endomembrane system;MPFO	O.I.	C.G.	H.G.
17.4	99.5	63.8	At2g40420	818635	amino acid transporter family protein	Encodes a putative amino acid transporter.	O.I.	C.G.	H.G.
17.4	99.5	17.2	At1g43590	840943	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
17.3	99.5	107.6	At2g37640	818341	EXP3	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.
17.2	99.5	93.7	At5g04470	830326	SIM (SIAMESE)	Encodes a novel nuclear 14-kD protein containing a cyclin binding motif and a motif found in ICK/KRP cell cycle inhibitor proteins. It is required for coordinating cell division and cell differentiation during the development of Arabidopsis trichomes, playing a key role in the mitosis-to-endoreduplication transition. It interacts with D-type cyclins in vivo.	O.I.	C.G.	H.G.
17.2	99.5	40.7	At5g24170	832484	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFP	O.I.	C.G.	H.G.
16.9	99.5	222.9	At3g12610	820441	DRT100 (DNA-DAMAGE REPAIR/TOLERATION 100)	Plays role in DNA-damage repair/toleration. Partially complements RecA- phenotypes.	O.I.	C.G.	H.G.
16.7	99.5	61.2	At2g27370	817280	integral membrane family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
16.6	99.5	265.3	At4g21850	828273	methionine sulfoxide reductase domain-containing protein / SeIR domain-containing protein	F:peptide-methionine-(S)-S-oxide reductase activity;P:biological_process unknown;C:cellular_component unknown;OBMPFAV	O.I.	C.G.	H.G.
16.5	99.5	48.2	At3g62860	825461	esterase/lipase/thioesterase family protein	F:catalytic activity;P:unknown;C:plasma membrane;BOPMFVA	O.I.	C.G.	H.G.
16.4	99.5	121.0	At4g18970	827632	GDSL-motif lipase/hydrolase family protein	F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBFOM	O.I.	C.G.	H.G.
16.1	99.5	102.2	At2g34070	817968	unknown protein	F:unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
15.9	99.5	103.5	At1g75900	843923	family II extracellular lipase 3 (EXL3)	F:lipase activity, carboxylesterase activity, acyltransferase activity;P:sexual reproduction;C:extracellular region;PBFOM	O.I.	C.G.	H.G.
15.9	99.5	62.9	At2g47930	819405	AGP26 (ARABINOGALACTAN PROTEIN 26)	F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;OPMVBFA	O.I.	C.G.	H.G.
15.9	99.5	13.0	At1g27670	839659	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
15.7	99.5	58.0	At3g60530	825224	zinc finger (GATA type) family protein	F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;PFOM	O.I.	C.G.	H.G.
15.4	99.5	104.6	At5g22500	832311	FAR1 (FATTY ACID REDUCTASE 1)	F:oxidoreductase activity, acting on the CH-CH group of donors, fatty acyl-CoA reductase (alcohol-forming) activity;P:microsporogenesis, metabolic process;C:chloroplast;MBFOP	O.I.	C.G.	H.G.
15.4	99.5	32.7	At4g23870	828486	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
15.2	99.4	115.7	At4g20870	827835	FAH2 (FATTY ACID HYDROXYLASE 2)	encodes a fatty acid hydroxylase, required for the AtBI-1-mediated suppression of programmed cell death.	O.I.	C.G.	H.G.
15.2	99.4	62.5	At2g32690	3768391	GRP23 (GLYCINE-RICH PROTEIN 23)	Glycine-rich protein similar in structure to GRP5. The expression of GRP23 is induced by HPA (cutin monomer, salicylic acid, and abscisic acid.	O.I.	C.G.	H.G.
15.0	99.4	142.8	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.
14.9	99.4	172.5	At1g22530	838859	PATL2 (PATELLIN 2)	F:transporter activity;P:transport;C:plasma membrane, chloroplast;MOBFPVA	O.I.	C.G.	H.G.
14.9	99.4	47.4	At3g57790	824949	glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein	F:polygalacturonase activity;P:carbohydrate metabolic process;C:plasma membrane;PBFOMAV	O.I.	C.G.	H.G.
14.8	99.4	14.1	At2g22890	816820	small conjugating protein ligase	F:small conjugating protein ligase activity;P:regulation of protein metabolic process, post-translational protein modification;C:chloroplast;MOPBV	O.I.	C.G.	H.G.
14.6	99.4	305.2	At2g37130	818289	peroxidase 21 (PER21) (P21) (PRXR5)	F:electron carrier activity, peroxidase activity, heme binding;P:defense response to fungus;C:endomembrane system;PFO	O.I.	C.G.	H.G.
14.5	99.4	196.7	At2g36100	818183	integral membrane family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
14.5	99.4	116.9	At5g24570	832528	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	C.G.	H.G.
14.5	99.4	65.6	At5g41080	834110	glycerophosphoryl diester phosphodiesterase family protein	F:phosphoric diester hydrolase activity, glycerophosphodiester phosphodiesterase activity;P:glycerol metabolic process, lipid metabolic process;C:unknown;BOMFPAV	O.I.	C.G.	H.G.
14.4	99.4	348.0	At3g21720	821726	ICL (ISOCITRATE LYASE)	Encodes a glyoxylate cycle enzyme isocitrate lyase (ICL).	O.I.	C.G.	H.G.
14.4	99.4	27.4	At2g42900	818891	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM	O.I.	C.G.	H.G.

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GSM ID	GSM134518
Assay name	Col-0_4day_red illumination_-lincomycin_rep2
GSE experiment	GSE5759: red illumination w/o lincomycin

Microarray experiments to specifically-expressed genes

GSM ID GSM134518 Assay name Col-0_4day_red illumination_-lincomycin_rep2 GSE experiment GSE5759: red illumination w/o lincomycin

GSM ID GSM134518

Assay name Col-0_4day_red illumination_-lincomycin_rep2

GSE experiment GSE5759: red illumination w/o lincomycin