CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM134514

Assay name Col-0_4day_dark_-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
143.2 99.9 42.0 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.
79.3 99.9 132.3 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.
69.2 99.9 66.6 At5g53660 835447 AtGRF7 (GROWTH-REGULATING FACTOR 7) Growth regulating factor encoding transcription activator. One of the nine members of a GRF gene family, containing nuclear targeting domain. Involved in leaf development and expressed in shoot and flower. O.I. C.G. H.G.
65.9 99.8 174.6 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.
57.7 99.8 169.7 At1g67910 843119 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
54.3 99.8 148.7 At4g16515 827350 unknown protein F:molecular_function unknown;P:unknown;C:endomembrane system;P O.I. C.G. H.G.
51.8 99.8 41.2 At1g62610 842558 short-chain dehydrogenase/reductase (SDR) family protein F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:cellular_component unknown;BOMFPAV O.I. C.G. H.G.
50.6 99.8 80.0 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.
48.0 99.8 71.5 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.
47.0 99.8 44.3 At3g24450 822035 copper-binding family protein F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:endomembrane system;POM O.I. C.G. H.G.
46.1 99.8 71.0 At1g64670 842775 BDG1 (BODYGUARD1) Encodes a epidermally expressed extracellular protein that likely functions as an alpha-beta hydrolase and is required for normal cuticle formation. Homozygous mutant plants are dwarfed and have abnormal leaves, collapsed cells, reduced numbers of trichomes. The specific role of BDG is unclear: it may function in cutin biosynthesis or as a cross-linking enzyme in the cell wall itself. O.I. C.G. H.G.
45.7 99.8 52.8 At5g57240 835830 ORP4C (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 4C) F:oxysterol binding;P:steroid metabolic process;C:cellular_component unknown;MFOP O.I. C.G. H.G.
45.6 99.8 145.5 At5g54190 835507 PORA light-dependent NADPH:protochlorophyllide oxidoreductase A O.I. C.G. H.G.
45.5 99.8 168.6 At5g02020 831782 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
45.4 99.8 73.3 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.
43.4 99.8 83.6 At5g01320 830867 pyruvate decarboxylase, putative F:in 6 functions;P:unknown;C:cellular_component unknown;BOFPAMV O.I. C.G. H.G.
42.6 99.8 39.6 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.
41.9 99.8 116.1 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.
41.3 99.8 126.1 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.
40.8 99.8 136.8 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.
40.6 99.8 94.0 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.
40.1 99.8 21.5 At3g29370 822596 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
38.5 99.8 45.9 At2g34020 817963 calcium ion binding F:calcium ion binding;P:biological_process unknown;C:unknown;POMBF O.I. C.G. H.G.
36.5 99.7 61.4 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.
35.8 99.7 79.3 At5g53980 835481 ATHB52 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 52) Encodes a homeodomain leucine zipper class I (HD-Zip I) protein. O.I. C.G. H.G.
34.1 99.7 68.9 At1g22740 838880 RABG3B GTP-binding protein Rab7 O.I. C.G. H.G.
34.0 99.7 11.2 At3g03830 821123 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. C.G. H.G.
33.6 99.7 115.8 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.
33.6 99.7 107.0 At5g44440 834471 FAD-binding domain-containing protein F:electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity;P:unknown;C:endomembrane system;BFPOAM O.I. C.G. H.G.
33.5 99.7 62.8 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.
33.2 99.7 30.9 At3g54510 824616 early-responsive to dehydration protein-related / ERD protein-related F:unknown;P:unknown;C:endomembrane system, membrane;FPMO O.I. C.G. H.G.
32.9 99.7 269.3 At2g21140 816649 ATPRP2 (PROLINE-RICH PROTEIN 2) Proline-rich protein expressed in expanding leaves, stems, flowers, and siliques. O.I. C.G. H.G.
32.5 99.7 38.5 At5g15830 831440 AtbZIP3 (Arabidopsis thaliana basic leucine-zipper 3) F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;POMFB O.I. C.G. H.G.
31.7 99.7 156.2 At3g15540 820793 IAA19 (INDOLE-3-ACETIC ACID INDUCIBLE 19) IAA induced protein 19 O.I. C.G. H.G.
30.8 99.7 231.2 At5g60660 836187 PIP2 F:water channel activity;P:transport;C:integral to membrane, membrane;BPMOFAV O.I. C.G. H.G.
30.3 99.7 22.7 At1g43590 840943 transposable element gene F:unknown;P:unknown;C:unknown O.I. C.G. H.G.
30.2 99.7 6.3 At5g03310 831879 auxin-responsive family protein F:molecular_function unknown;P:response to auxin stimulus;C:unknown;P O.I. C.G. H.G.
30.0 99.7 22.4 At1g52250 - - O.I. C.G. H.G.
29.8 99.7 40.4 At2g20750 816604 ATEXPB1 (ARABIDOPSIS THALIANA EXPANSIN B1) member of BETA-EXPANSINS. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio) O.I. C.G. H.G.
29.5 99.7 19.3 At5g15150 831367 ATHB-3 (ARABIDOPSIS THALIANA HOMEOBOX 3) homeobox-containing gene with an unusual feature: a leucine zipper motif adjacent to the carboxyl-terminal of the homeodomain structure. This gene is expressed primarily in the cortex of the root and the stem. O.I. C.G. H.G.
29.3 99.7 174.9 At1g12080 837760 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA O.I. C.G. H.G.
29.3 99.7 45.1 At4g23870 828486 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
29.2 99.7 14.5 At2g46990 819313 IAA20 (INDOLE-3-ACETIC ACID INDUCIBLE 20) Encodes a member of the Aux/IAA family of proteins implicated in auxin signaling. IAA20 lacks the conserved degron (domain II) found in many family members, and IAA20 fusion proteins are stable in Arabidopsis seedlings. IAA20 transcripts are induced by auxin treatment, and overexpression of IAA20 leads to defects in gravitropism, root development, root meristem maintenance, etiolation, and cotyledon vascular development. O.I. C.G. H.G.
28.9 99.7 61.8 At5g63650 836485 SNRK2.5 (SNF1-RELATED PROTEIN KINASE 2.5) encodes a member of SNF1-related protein kinases (SnRK2) whose activity is activated by ionic (salt) and non-ionic (mannitol) osmotic stress. O.I. C.G. H.G.
28.4 99.7 36.9 At5g59010 836018 protein kinase-related F:protein tyrosine kinase activity, binding, protein kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;PMBOFVA O.I. C.G. H.G.
28.2 99.7 12.0 At5g49800 835043 - F:molecular_function unknown;P:biological_process unknown;C:unknown;MOPBF O.I. C.G. H.G.
28.1 99.7 13.5 At2g14060 815891 S-adenosyl-L-methionine:carboxyl methyltransferase family protein encodes a protein whose sequence is similar to SAM:salicylic acid carboxyl methyltransferase (SAMT) (GI:6002712)(Clarkia breweri) and to SAM:benzoic acid carboxyl methyltransferase (BAMT)(GI:9789277)(Antirrhinum majus) O.I. C.G. H.G.
28.0 99.7 62.9 At3g62860 825461 esterase/lipase/thioesterase family protein F:catalytic activity;P:unknown;C:plasma membrane;BOPMFVA O.I. C.G. H.G.
27.8 99.7 38.1 At2g42900 818891 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM O.I. C.G. H.G.
27.2 99.7 32.4 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.
26.6 99.7 30.2 At4g30410 829164 transcription factor F:transcription factor activity;P:unknown;C:unknown;PO O.I. C.G. H.G.
26.5 99.7 92.3 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.
26.5 99.7 22.4 At2g21830 816719 DC1 domain-containing protein F:protein binding, zinc ion binding;P:intracellular signaling cascade;C:unknown;PMO O.I. C.G. H.G.
26.4 99.7 89.0 At3g21090 821661 ABC transporter family protein F:ATPase activity, coupled to transmembrane movement of substances;P:transport;C:membrane;BOMFAPV O.I. C.G. H.G.
26.0 99.7 91.8 At1g15350 838104 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;PO O.I. C.G. H.G.
26.0 99.7 33.3 At1g34110 840310 leucine-rich repeat transmembrane protein kinase, putative F:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA O.I. C.G. H.G.
25.5 99.7 128.7 At2g34070 817968 unknown protein F:unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
25.5 99.7 107.7 At4g01950 827165 GPAT3 (GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE 3) Encodes a member of a family of proteins with glycerol-3-phosphate acyltransferase activity. O.I. C.G. H.G.
25.3 99.6 36.7 At4g35720 829724 unknown protein F:unknown;P:unknown;C:unknown;PO O.I. C.G. H.G.
24.9 99.6 309.3 At4g14130 827051 XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7) xyloglucan endotransglycosylase-related protein (XTR7) O.I. C.G. H.G.
24.7 99.6 234.4 At5g53250 835406 AGP22 (ARABINOGALACTAN PROTEIN 22) F:unknown;P:unknown;C:anchored to membrane;P O.I. C.G. H.G.
24.7 99.6 148.7 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.
24.6 99.6 203.6 At1g32170 840109 XTR4 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 4) xyloglucan endotransglycosylase-related protein (XTR4) O.I. C.G. H.G.
24.3 99.6 120.0 At1g75780 843911 TUB1 beta tubulin gene downregulated by phytochrome A (phyA)-mediated far-red light high-irradiance and the phytochrome B (phyB)-mediated red light high-irradiance responses O.I. C.G. H.G.
24.2 99.6 37.8 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.
24.0 99.6 94.7 At4g25830 828688 integral membrane family protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
23.7 99.6 41.6 At2g21880 816724 ATRAB7A F:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:unknown;MOFPBVA O.I. C.G. H.G.
23.3 99.6 109.6 At5g04120 830290 phosphoglycerate/bisphosphoglycerate mutase family protein F:catalytic activity;P:metabolic process;C:cellular_component unknown;BOMFPA O.I. C.G. H.G.
23.2 99.6 21.4 At4g37580 829913 HLS1 (HOOKLESS 1) involved in apical hook development. putative N-acetyltransferase O.I. C.G. H.G.
22.7 99.6 113.4 At1g29090 839784 peptidase C1A papain family protein F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis;C:endomembrane system;MOPVBAF O.I. C.G. H.G.
22.7 99.6 54.1 At4g21600 828246 ENDO5 (endonuclease 5) Encodes a protein with mismatch-specific endonuclease activity with a preference for T/G, A/G, and G/G of single base mismatches. It also has the ability to cleave indel types of mismatches (heteroduplexes with loops). O.I. C.G. H.G.
22.7 99.6 21.7 At4g10910 826689 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
22.6 99.6 127.0 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.
22.6 99.6 76.1 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.
22.4 99.6 15.9 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.
22.2 99.6 122.4 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.
21.9 99.6 163.3 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.
21.7 99.6 54.1 At3g18200 821347 nodulin MtN21 family protein F:molecular_function unknown;P:unknown;C:endomembrane system, membrane;BOPAMF O.I. C.G. H.G.
21.6 99.6 41.8 At2g28350 817382 ARF10 (AUXIN RESPONSE FACTOR 10) Involved in root cap cell differentiation. O.I. C.G. H.G.
21.4 99.6 241.3 At4g32460 829381 - F:molecular_function unknown;P:biological_process unknown;C:plant-type cell wall;PB O.I. C.G. H.G.
21.1 99.6 79.9 At1g65310 842839 XTH17 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 17) putative xyloglucan endotransglycosylase/hydrolase, expressed in the mature or basal regions of both the main and lateral roots, but not in the tip of these roots where cell division occurs. O.I. C.G. H.G.
21.1 99.6 11.0 At3g03840 821121 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. C.G. H.G.
20.9 99.6 23.6 At3g60390 825210 HAT3 (HOMEOBOX-LEUCINE ZIPPER PROTEIN 3) Encodes homeobox protein HAT3. O.I. C.G. H.G.
20.7 99.6 44.0 At2g44740 819082 CYCP4 F:cyclin-dependent protein kinase activity;P:regulation of cell cycle;C:unknown;FOMPB O.I. C.G. H.G.
20.7 99.6 14.2 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.
20.6 99.6 148.0 At2g18280 816344 AtTLP2 (TUBBY LIKE PROTEIN 2) Member of TLP family O.I. C.G. H.G.
20.6 99.6 74.1 At3g12710 820453 methyladenine glycosylase family protein F:DNA-3-methyladenine glycosylase I activity, catalytic activity;P:DNA repair, base-excision repair;C:unknown;BOPAM O.I. C.G. H.G.
20.6 99.6 37.1 At1g78260 844161 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.
20.6 99.6 28.4 At4g16670 827369 phosphoinositide binding F:phosphoinositide binding;P:signal transduction;C:cellular_component unknown;PFO O.I. C.G. H.G.
20.5 99.6 51.4 At1g69526 843287 UbiE/COQ5 methyltransferase family protein F:methyltransferase activity;P:unknown;C:chloroplast;PBO O.I. C.G. H.G.
20.4 99.6 39.1 At1g05810 837091 RABA5E (RAB GTPASE HOMOLOG A5E) F:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:chloroplast;MOFPBVA O.I. C.G. H.G.
20.3 99.6 92.1 At4g28050 828920 TET7 (TETRASPANIN7) Member of TETRASPANIN family O.I. C.G. H.G.
20.1 99.6 65.4 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.
20.0 99.6 49.6 At4g34250 829574 KCS16 (3-KETOACYL-COA SYNTHASE 16) Encodes KCS16, 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.
20.0 99.6 34.1 At5g01075 831885 beta-galactosidase F:beta-galactosidase activity;P:carbohydrate metabolic process;C:endomembrane system, beta-galactosidase complex;P O.I. C.G. H.G.
19.5 99.6 30.8 At1g52830 841717 IAA6 (INDOLE-3-ACETIC ACID 6) An extragenic dominant suppressor of the hy2 mutant phenotype. Also exhibits aspects of constitutive photomorphogenetic phenotype in the absence of hy2. Mutants have dominant leaf curling phenotype shortened hypocotyls and reduced apical hook. Induced by indole-3-acetic acid. O.I. C.G. H.G.
19.4 99.6 75.8 At5g16590 831521 LRR1 F:protein serine/threonine kinase activity, kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation, response to symbiotic fungus;C:plasma membrane, membrane, plant-type cell wall;PMOBFVA O.I. C.G. H.G.
19.2 99.6 23.1 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.
19.2 99.6 15.1 At1g70270 843363 ATP binding / DNA binding F:DNA binding, ATP binding;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
19.1 99.6 134.1 At5g24570 832528 unknown protein F:molecular_function unknown;P:biological_process 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.
143.2	99.9	42.0	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.
79.3	99.9	132.3	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.
69.2	99.9	66.6	At5g53660	835447	AtGRF7 (GROWTH-REGULATING FACTOR 7)	Growth regulating factor encoding transcription activator. One of the nine members of a GRF gene family, containing nuclear targeting domain. Involved in leaf development and expressed in shoot and flower.	O.I.	C.G.	H.G.
65.9	99.8	174.6	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.
57.7	99.8	169.7	At1g67910	843119	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
54.3	99.8	148.7	At4g16515	827350	unknown protein	F:molecular_function unknown;P:unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
51.8	99.8	41.2	At1g62610	842558	short-chain dehydrogenase/reductase (SDR) family protein	F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:cellular_component unknown;BOMFPAV	O.I.	C.G.	H.G.
50.6	99.8	80.0	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.
48.0	99.8	71.5	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.
47.0	99.8	44.3	At3g24450	822035	copper-binding family protein	F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:endomembrane system;POM	O.I.	C.G.	H.G.
46.1	99.8	71.0	At1g64670	842775	BDG1 (BODYGUARD1)	Encodes a epidermally expressed extracellular protein that likely functions as an alpha-beta hydrolase and is required for normal cuticle formation. Homozygous mutant plants are dwarfed and have abnormal leaves, collapsed cells, reduced numbers of trichomes. The specific role of BDG is unclear: it may function in cutin biosynthesis or as a cross-linking enzyme in the cell wall itself.	O.I.	C.G.	H.G.
45.7	99.8	52.8	At5g57240	835830	ORP4C (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 4C)	F:oxysterol binding;P:steroid metabolic process;C:cellular_component unknown;MFOP	O.I.	C.G.	H.G.
45.6	99.8	145.5	At5g54190	835507	PORA	light-dependent NADPH:protochlorophyllide oxidoreductase A	O.I.	C.G.	H.G.
45.5	99.8	168.6	At5g02020	831782	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
45.4	99.8	73.3	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.
43.4	99.8	83.6	At5g01320	830867	pyruvate decarboxylase, putative	F:in 6 functions;P:unknown;C:cellular_component unknown;BOFPAMV	O.I.	C.G.	H.G.
42.6	99.8	39.6	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.
41.9	99.8	116.1	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.
41.3	99.8	126.1	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.
40.8	99.8	136.8	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.
40.6	99.8	94.0	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.
40.1	99.8	21.5	At3g29370	822596	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
38.5	99.8	45.9	At2g34020	817963	calcium ion binding	F:calcium ion binding;P:biological_process unknown;C:unknown;POMBF	O.I.	C.G.	H.G.
36.5	99.7	61.4	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.
35.8	99.7	79.3	At5g53980	835481	ATHB52 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 52)	Encodes a homeodomain leucine zipper class I (HD-Zip I) protein.	O.I.	C.G.	H.G.
34.1	99.7	68.9	At1g22740	838880	RABG3B	GTP-binding protein Rab7	O.I.	C.G.	H.G.
34.0	99.7	11.2	At3g03830	821123	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	C.G.	H.G.
33.6	99.7	115.8	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.
33.6	99.7	107.0	At5g44440	834471	FAD-binding domain-containing protein	F:electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity;P:unknown;C:endomembrane system;BFPOAM	O.I.	C.G.	H.G.
33.5	99.7	62.8	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.
33.2	99.7	30.9	At3g54510	824616	early-responsive to dehydration protein-related / ERD protein-related	F:unknown;P:unknown;C:endomembrane system, membrane;FPMO	O.I.	C.G.	H.G.
32.9	99.7	269.3	At2g21140	816649	ATPRP2 (PROLINE-RICH PROTEIN 2)	Proline-rich protein expressed in expanding leaves, stems, flowers, and siliques.	O.I.	C.G.	H.G.
32.5	99.7	38.5	At5g15830	831440	AtbZIP3 (Arabidopsis thaliana basic leucine-zipper 3)	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;POMFB	O.I.	C.G.	H.G.
31.7	99.7	156.2	At3g15540	820793	IAA19 (INDOLE-3-ACETIC ACID INDUCIBLE 19)	IAA induced protein 19	O.I.	C.G.	H.G.
30.8	99.7	231.2	At5g60660	836187	PIP2	F:water channel activity;P:transport;C:integral to membrane, membrane;BPMOFAV	O.I.	C.G.	H.G.
30.3	99.7	22.7	At1g43590	840943	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	C.G.	H.G.
30.2	99.7	6.3	At5g03310	831879	auxin-responsive family protein	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;P	O.I.	C.G.	H.G.
30.0	99.7	22.4	At1g52250		-	-	O.I.	C.G.	H.G.
29.8	99.7	40.4	At2g20750	816604	ATEXPB1 (ARABIDOPSIS THALIANA EXPANSIN B1)	member of BETA-EXPANSINS. Naming convention from the Expansin Working Group (Kende et al, 2004. Plant Mol Bio)	O.I.	C.G.	H.G.
29.5	99.7	19.3	At5g15150	831367	ATHB-3 (ARABIDOPSIS THALIANA HOMEOBOX 3)	homeobox-containing gene with an unusual feature: a leucine zipper motif adjacent to the carboxyl-terminal of the homeodomain structure. This gene is expressed primarily in the cortex of the root and the stem.	O.I.	C.G.	H.G.
29.3	99.7	174.9	At1g12080	837760	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA	O.I.	C.G.	H.G.
29.3	99.7	45.1	At4g23870	828486	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
29.2	99.7	14.5	At2g46990	819313	IAA20 (INDOLE-3-ACETIC ACID INDUCIBLE 20)	Encodes a member of the Aux/IAA family of proteins implicated in auxin signaling. IAA20 lacks the conserved degron (domain II) found in many family members, and IAA20 fusion proteins are stable in Arabidopsis seedlings. IAA20 transcripts are induced by auxin treatment, and overexpression of IAA20 leads to defects in gravitropism, root development, root meristem maintenance, etiolation, and cotyledon vascular development.	O.I.	C.G.	H.G.
28.9	99.7	61.8	At5g63650	836485	SNRK2.5 (SNF1-RELATED PROTEIN KINASE 2.5)	encodes a member of SNF1-related protein kinases (SnRK2) whose activity is activated by ionic (salt) and non-ionic (mannitol) osmotic stress.	O.I.	C.G.	H.G.
28.4	99.7	36.9	At5g59010	836018	protein kinase-related	F:protein tyrosine kinase activity, binding, protein kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;PMBOFVA	O.I.	C.G.	H.G.
28.2	99.7	12.0	At5g49800	835043	-	F:molecular_function unknown;P:biological_process unknown;C:unknown;MOPBF	O.I.	C.G.	H.G.
28.1	99.7	13.5	At2g14060	815891	S-adenosyl-L-methionine:carboxyl methyltransferase family protein	encodes a protein whose sequence is similar to SAM:salicylic acid carboxyl methyltransferase (SAMT) (GI:6002712)(Clarkia breweri) and to SAM:benzoic acid carboxyl methyltransferase (BAMT)(GI:9789277)(Antirrhinum majus)	O.I.	C.G.	H.G.
28.0	99.7	62.9	At3g62860	825461	esterase/lipase/thioesterase family protein	F:catalytic activity;P:unknown;C:plasma membrane;BOPMFVA	O.I.	C.G.	H.G.
27.8	99.7	38.1	At2g42900	818891	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM	O.I.	C.G.	H.G.
27.2	99.7	32.4	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.
26.6	99.7	30.2	At4g30410	829164	transcription factor	F:transcription factor activity;P:unknown;C:unknown;PO	O.I.	C.G.	H.G.
26.5	99.7	92.3	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.
26.5	99.7	22.4	At2g21830	816719	DC1 domain-containing protein	F:protein binding, zinc ion binding;P:intracellular signaling cascade;C:unknown;PMO	O.I.	C.G.	H.G.
26.4	99.7	89.0	At3g21090	821661	ABC transporter family protein	F:ATPase activity, coupled to transmembrane movement of substances;P:transport;C:membrane;BOMFAPV	O.I.	C.G.	H.G.
26.0	99.7	91.8	At1g15350	838104	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;PO	O.I.	C.G.	H.G.
26.0	99.7	33.3	At1g34110	840310	leucine-rich repeat transmembrane protein kinase, putative	F:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVA	O.I.	C.G.	H.G.
25.5	99.7	128.7	At2g34070	817968	unknown protein	F:unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
25.5	99.7	107.7	At4g01950	827165	GPAT3 (GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE 3)	Encodes a member of a family of proteins with glycerol-3-phosphate acyltransferase activity.	O.I.	C.G.	H.G.
25.3	99.6	36.7	At4g35720	829724	unknown protein	F:unknown;P:unknown;C:unknown;PO	O.I.	C.G.	H.G.
24.9	99.6	309.3	At4g14130	827051	XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7)	xyloglucan endotransglycosylase-related protein (XTR7)	O.I.	C.G.	H.G.
24.7	99.6	234.4	At5g53250	835406	AGP22 (ARABINOGALACTAN PROTEIN 22)	F:unknown;P:unknown;C:anchored to membrane;P	O.I.	C.G.	H.G.
24.7	99.6	148.7	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.
24.6	99.6	203.6	At1g32170	840109	XTR4 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 4)	xyloglucan endotransglycosylase-related protein (XTR4)	O.I.	C.G.	H.G.
24.3	99.6	120.0	At1g75780	843911	TUB1	beta tubulin gene downregulated by phytochrome A (phyA)-mediated far-red light high-irradiance and the phytochrome B (phyB)-mediated red light high-irradiance responses	O.I.	C.G.	H.G.
24.2	99.6	37.8	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.
24.0	99.6	94.7	At4g25830	828688	integral membrane family protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
23.7	99.6	41.6	At2g21880	816724	ATRAB7A	F:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:unknown;MOFPBVA	O.I.	C.G.	H.G.
23.3	99.6	109.6	At5g04120	830290	phosphoglycerate/bisphosphoglycerate mutase family protein	F:catalytic activity;P:metabolic process;C:cellular_component unknown;BOMFPA	O.I.	C.G.	H.G.
23.2	99.6	21.4	At4g37580	829913	HLS1 (HOOKLESS 1)	involved in apical hook development. putative N-acetyltransferase	O.I.	C.G.	H.G.
22.7	99.6	113.4	At1g29090	839784	peptidase C1A papain family protein	F:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis;C:endomembrane system;MOPVBAF	O.I.	C.G.	H.G.
22.7	99.6	54.1	At4g21600	828246	ENDO5 (endonuclease 5)	Encodes a protein with mismatch-specific endonuclease activity with a preference for T/G, A/G, and G/G of single base mismatches. It also has the ability to cleave indel types of mismatches (heteroduplexes with loops).	O.I.	C.G.	H.G.
22.7	99.6	21.7	At4g10910	826689	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
22.6	99.6	127.0	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.
22.6	99.6	76.1	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.
22.4	99.6	15.9	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.
22.2	99.6	122.4	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.
21.9	99.6	163.3	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.
21.7	99.6	54.1	At3g18200	821347	nodulin MtN21 family protein	F:molecular_function unknown;P:unknown;C:endomembrane system, membrane;BOPAMF	O.I.	C.G.	H.G.
21.6	99.6	41.8	At2g28350	817382	ARF10 (AUXIN RESPONSE FACTOR 10)	Involved in root cap cell differentiation.	O.I.	C.G.	H.G.
21.4	99.6	241.3	At4g32460	829381	-	F:molecular_function unknown;P:biological_process unknown;C:plant-type cell wall;PB	O.I.	C.G.	H.G.
21.1	99.6	79.9	At1g65310	842839	XTH17 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 17)	putative xyloglucan endotransglycosylase/hydrolase, expressed in the mature or basal regions of both the main and lateral roots, but not in the tip of these roots where cell division occurs.	O.I.	C.G.	H.G.
21.1	99.6	11.0	At3g03840	821121	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	C.G.	H.G.
20.9	99.6	23.6	At3g60390	825210	HAT3 (HOMEOBOX-LEUCINE ZIPPER PROTEIN 3)	Encodes homeobox protein HAT3.	O.I.	C.G.	H.G.
20.7	99.6	44.0	At2g44740	819082	CYCP4	F:cyclin-dependent protein kinase activity;P:regulation of cell cycle;C:unknown;FOMPB	O.I.	C.G.	H.G.
20.7	99.6	14.2	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.
20.6	99.6	148.0	At2g18280	816344	AtTLP2 (TUBBY LIKE PROTEIN 2)	Member of TLP family	O.I.	C.G.	H.G.
20.6	99.6	74.1	At3g12710	820453	methyladenine glycosylase family protein	F:DNA-3-methyladenine glycosylase I activity, catalytic activity;P:DNA repair, base-excision repair;C:unknown;BOPAM	O.I.	C.G.	H.G.
20.6	99.6	37.1	At1g78260	844161	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.
20.6	99.6	28.4	At4g16670	827369	phosphoinositide binding	F:phosphoinositide binding;P:signal transduction;C:cellular_component unknown;PFO	O.I.	C.G.	H.G.
20.5	99.6	51.4	At1g69526	843287	UbiE/COQ5 methyltransferase family protein	F:methyltransferase activity;P:unknown;C:chloroplast;PBO	O.I.	C.G.	H.G.
20.4	99.6	39.1	At1g05810	837091	RABA5E (RAB GTPASE HOMOLOG A5E)	F:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:chloroplast;MOFPBVA	O.I.	C.G.	H.G.
20.3	99.6	92.1	At4g28050	828920	TET7 (TETRASPANIN7)	Member of TETRASPANIN family	O.I.	C.G.	H.G.
20.1	99.6	65.4	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.
20.0	99.6	49.6	At4g34250	829574	KCS16 (3-KETOACYL-COA SYNTHASE 16)	Encodes KCS16, 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.
20.0	99.6	34.1	At5g01075	831885	beta-galactosidase	F:beta-galactosidase activity;P:carbohydrate metabolic process;C:endomembrane system, beta-galactosidase complex;P	O.I.	C.G.	H.G.
19.5	99.6	30.8	At1g52830	841717	IAA6 (INDOLE-3-ACETIC ACID 6)	An extragenic dominant suppressor of the hy2 mutant phenotype. Also exhibits aspects of constitutive photomorphogenetic phenotype in the absence of hy2. Mutants have dominant leaf curling phenotype shortened hypocotyls and reduced apical hook. Induced by indole-3-acetic acid.	O.I.	C.G.	H.G.
19.4	99.6	75.8	At5g16590	831521	LRR1	F:protein serine/threonine kinase activity, kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation, response to symbiotic fungus;C:plasma membrane, membrane, plant-type cell wall;PMOBFVA	O.I.	C.G.	H.G.
19.2	99.6	23.1	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.
19.2	99.6	15.1	At1g70270	843363	ATP binding / DNA binding	F:DNA binding, ATP binding;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
19.1	99.6	134.1	At5g24570	832528	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	C.G.	H.G.

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GSM ID	GSM134514
Assay name	Col-0_4day_dark_-lincomycin_rep2
GSE experiment	GSE5759: red illumination w/o lincomycin

Microarray experiments to specifically-expressed genes

GSM ID GSM134514 Assay name Col-0_4day_dark_-lincomycin_rep2 GSE experiment GSE5759: red illumination w/o lincomycin

GSM ID GSM134514

Assay name Col-0_4day_dark_-lincomycin_rep2

GSE experiment GSE5759: red illumination w/o lincomycin