CoP: Co-expressed Biological Processes

Microarray experiments to specifically-expressed genes

GSM ID GSM292076

Assay name Wt, dark sample, biological rep1

GSE experiment GSE11594: Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings

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
62.6 99.8 159.6 At4g16515 827350 unknown protein F:molecular_function unknown;P:unknown;C:endomembrane system;P O.I. C.G. H.G.
59.7 99.8 142.6 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.
55.8 99.8 306.6 At1g32170 840109 XTR4 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 4) xyloglucan endotransglycosylase-related protein (XTR4) O.I. C.G. H.G.
54.1 99.8 216.9 At4g37220 829876 stress-responsive protein, putative F:molecular_function unknown;P:response to fructose stimulus, response to sucrose stimulus, response to glucose stimulus, response to stress;C:cellular_component unknown;P O.I. C.G. H.G.
50.7 99.8 287.4 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.
40.8 99.8 170.5 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.
40.0 99.8 52.7 At4g23870 828486 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
37.1 99.7 131.2 At5g54190 835507 PORA light-dependent NADPH:protochlorophyllide oxidoreductase A O.I. C.G. H.G.
36.7 99.7 151.3 At5g02020 831782 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
35.1 99.7 367.7 At4g14130 827051 XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7) xyloglucan endotransglycosylase-related protein (XTR7) O.I. C.G. H.G.
34.9 99.7 24.1 At1g52250 - - O.I. C.G. H.G.
34.0 99.7 93.3 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.
33.9 99.7 294.6 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.
33.0 99.7 103.0 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.
32.3 99.7 28.0 At1g29450 839821 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;P O.I. C.G. H.G.
32.2 99.7 31.4 At2g45050 819112 zinc finger (GATA type) family protein F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;FPMOV O.I. C.G. H.G.
32.1 99.7 61.8 At5g18060 831310 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. C.G. H.G.
31.9 99.7 289.0 At5g10430 830907 AGP4 (ARABINOGALACTAN PROTEIN 4) Encodes arabinogalactan-protein (AGP4). O.I. C.G. H.G.
31.5 99.7 120.7 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.
30.7 99.7 201.9 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.
30.6 99.7 373.9 At5g09440 830803 EXL4 (EXORDIUM LIKE 4) F:molecular_function unknown;P:biological_process unknown;C:membrane;PB O.I. C.G. H.G.
29.7 99.7 165.7 At3g06850 819869 BCE2 dihydrolipoamide branched chain acyltransferase O.I. C.G. H.G.
28.2 99.7 24.2 At4g10910 826689 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
28.1 99.7 220.9 At5g60660 836187 PIP2 F:water channel activity;P:transport;C:integral to membrane, membrane;BPMOFAV O.I. C.G. H.G.
28.1 99.7 35.8 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.
28.0 99.7 69.7 At1g02340 839300 HFR1 (LONG HYPOCOTYL IN FAR-RED) Encodes a light-inducible, nuclear bHLH protein involved in phytochrome signaling. Mutants exhibit a long-hypocotyl phenotype only under far-red light but not under red light and are defective in other phytochrome A-related responses. Mutants also show blue light response defects. HFR1 interacts with COP1, co-localizes to the nuclear specks and is ubiquinated by COP1. O.I. C.G. H.G.
27.6 99.7 62.0 At1g22740 838880 RABG3B GTP-binding protein Rab7 O.I. C.G. H.G.
26.9 99.7 148.4 At2g44130 819019 kelch repeat-containing F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPBOFAV O.I. C.G. H.G.
26.5 99.7 166.3 At1g12080 837760 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA O.I. C.G. H.G.
26.2 99.7 16.7 At1g27670 839659 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
25.1 99.6 73.2 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.
25.0 99.6 349.7 At5g56870 835789 BGAL4 (beta-galactosidase 4) F:beta-galactosidase activity;P:lactose catabolic process, using glucoside 3-dehydrogenase, carbohydrate metabolic process, lactose catabolic process via UDP-galactose, lactose catabolic process;C:endomembrane system, beta-galactosidase complex;PBMFOA O.I. C.G. H.G.
24.3 99.6 394.2 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.
24.3 99.6 287.2 At3g61260 825298 DNA-binding family protein / remorin family protein F:binding;P:biological_process unknown;C:plasma membrane, vacuole;OBMFPVA O.I. C.G. H.G.
24.1 99.6 30.4 At4g39070 830062 zinc finger (B-box type) family protein F:transcription factor activity, zinc ion binding;P:response to chitin, regulation of transcription;C:intracellular;POM O.I. C.G. H.G.
23.9 99.6 416.4 At2g05540 815103 glycine-rich protein F:unknown;P:unknown;C:endomembrane system;MPBOFVA O.I. C.G. H.G.
23.1 99.6 19.6 At4g14380 827082 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;POM O.I. C.G. H.G.
23.0 99.6 128.8 At2g34500 818013 CYP710A1 (cytochrome P450, family 710, subfamily A, polypeptide 1) Encodes a protein with C22-sterol desaturase activity. The enzyme was shown to catalyze in the presence of NADPH the conversion of β-sitosterol to stigmasterol, but not that of 24-epi-campesterol to brassicasterol (unlike CYP710A2). O.I. C.G. H.G.
22.8 99.6 106.8 At1g67910 843119 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P O.I. C.G. H.G.
22.7 99.6 270.7 At3g23050 821879 IAA7 (INDOLE-3-ACETIC ACID 7) Transcription regulator acting as repressor of auxin-inducible gene expression. Plays role in the control of gravitropic growth and development in light-grown seedlings. Auxin induces the degradation of the protein in a dosage-dependent manner in a process mediated by AtRac1. Auxin induced the relocalization of the protein within the nucleus from a diffused nucleoplasmic pattern to a discrete particulated pattern named nuclear protein bodies or NPB in a process also mediated by Rac1. Colocalizes with SCF, CSN and 26S proteasome components. O.I. C.G. H.G.
22.6 99.6 247.2 At3g26510 822258 octicosapeptide/Phox/Bem1p (PB1) domain-containing protein F:unknown;P:biological_process unknown;C:unknown;POFMBV O.I. C.G. H.G.
22.4 99.6 244.0 At5g65390 836664 AGP7 F:unknown;P:unknown;C:anchored to membrane;BMOPFVA O.I. C.G. H.G.
22.3 99.6 70.9 At2g28110 817357 FRA8 (FRAGILE FIBER 8) Homolog to AT5G22940, a member of glycosyltransferase family 47 that is involved in secondary cell wall biosynthesis. It exhibits high sequence similarity to tobacco (Nicotiana plumbaginifolia) pectin glucuronyltransferase. Protein has a domain that shares significant similarity with the pfam03016 domain. It is expressed specifically in developing vessels and fiber cells, and FRA8 is targeted to Golgi. Mutants have irregular xylem formation, reduced cellulose levels and plants are smaller than normal siblings. O.I. C.G. H.G.
22.2 99.6 176.8 At2g17710 816280 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
22.1 99.6 153.7 At1g10070 837543 ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2) Encodes a chloroplast branched-chain amino acid aminotransferase. Complements the yeast leu/iso-leu/val auxotrophy mutant. O.I. C.G. H.G.
21.8 99.6 73.2 At3g05900 819759 neurofilament protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAV O.I. C.G. H.G.
21.6 99.6 179.1 At3g52060 824369 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POB O.I. C.G. H.G.
21.3 99.6 51.1 At2g28200 817366 nucleic acid binding / transcription factor/ zinc ion binding F:transcription factor activity, zinc ion binding, nucleic acid binding;P:regulation of transcription;C:intracellular;MPOF O.I. C.G. H.G.
21.2 99.6 151.5 At1g03090 838362 MCCA MCCA is the biotinylated subunit of the dimer MCCase, which is involved in leucine degradation. Both subunits are nuclear coded and the active enzyme is located in the mitochondrion. O.I. C.G. H.G.
21.0 99.6 86.4 At4g28270 828942 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;MPFOV O.I. C.G. H.G.
21.0 99.6 69.9 At3g49790 824141 ATP binding F:ATP binding;P:biological_process unknown;C:unknown;P O.I. C.G. H.G.
20.8 99.6 27.1 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.
20.4 99.6 212.6 At1g08510 837372 FATB (fatty acyl-ACP thioesterases B) Encodes an acyl-acyl carrier protein thioesterase. Hydrolyzes primarily saturated acyl-ACPs with chain lengths that vary between 8 and 18 carbons. Involved in saturated fatty acid synthesis. Nuclear-encoded, plastid-targeted globular protein that is functional as dimer. O.I. C.G. H.G.
20.4 99.6 116.1 At1g64660 842774 ATMGL (ARABIDOPSIS THALIANA METHIONINE GAMMA-LYASE) Encodes a functional methionine gamma-lyase, a cytosolic enzyme catalyzes the degradation of methionine into methanethiol, alpha-ketobutyrate and ammonia. The catabolism of excess methionine is important to methionine homeostasis. O.I. C.G. H.G.
20.3 99.6 41.4 At1g29500 839827 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:nucleolus, nucleus;P O.I. C.G. H.G.
20.1 99.6 82.3 At3g29575 822619 AFP3 (ABI FIVE BINDING PROTEIN 3) F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POM O.I. C.G. H.G.
20.1 99.6 15.7 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.
19.8 99.6 16.9 At4g36900 829843 RAP2.10 (related to AP2 10) encodes a member of the DREB subfamily A-5 of ERF/AP2 transcription factor family (RAP2.10). The protein contains one AP2 domain. There are 16 members in this subfamily including RAP2.9 and RAP2.1. O.I. C.G. H.G.
19.7 99.6 179.3 At3g61060 825278 AtPP2-A13 (Arabidopsis thaliana phloem protein 2-A13) F:carbohydrate binding;P:N-terminal protein myristoylation, response to wounding;C:unknown;P O.I. C.G. H.G.
19.5 99.6 208.5 At5g53250 835406 AGP22 (ARABINOGALACTAN PROTEIN 22) F:unknown;P:unknown;C:anchored to membrane;P O.I. C.G. H.G.
19.5 99.6 201.6 At5g18650 831983 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFA O.I. C.G. H.G.
19.3 99.6 14.4 At1g21360 838735 GLTP2 (glycolipid transfer protein 2) F:glycolipid transporter activity, glycolipid binding;P:glycolipid transport;C:cytoplasm;P O.I. C.G. H.G.
19.2 99.6 75.4 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.
19.1 99.6 192.3 At1g04250 839568 AXR3 (AUXIN RESISTANT 3) Transcription regulator acting as repressor of auxin-inducible gene expression. Auxin-inducible AUX/IAA gene. Short-lived nuclear protein with four conserved domains. Domain III has homology to beta alpha alpha dimerization and DNA binding domains. Involved in auxin signaling. Auxin induces the degradation of the protein in a dosage-dependent manner in a process mediated by AtRac1. Auxin induced the relocalization of the protein within the nucleus from a diffused nucleoplasmic pattern to a discrete particulated pattern named nuclear protein bodies or NPB in a process also mediated by Rac1. Colocalizes with SCF, CSN and 26S proteasome components. O.I. C.G. H.G.
19.0 99.5 34.6 At2g41850 818785 PGAZAT (POLYGALACTURONASE ABSCISSION ZONE A. THALIANA) ADPG2. O.I. C.G. H.G.
18.9 99.5 35.6 At3g59690 825138 IQD13 (IQ-domain 13) F:calmodulin binding;P:unknown;C:plasma membrane;POMVFB O.I. C.G. H.G.
18.7 99.5 202.9 At2g21140 816649 ATPRP2 (PROLINE-RICH PROTEIN 2) Proline-rich protein expressed in expanding leaves, stems, flowers, and siliques. O.I. C.G. H.G.
18.6 99.5 55.5 At1g02860 839559 NLA (nitrogen limitation adaptation) Encodes a likely ubiquitin E3 ligase with RING and SPX domains that is involved in mediating immune responses. O.I. C.G. H.G.
18.6 99.5 33.7 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.
18.1 99.5 96.1 At4g34760 829628 auxin-responsive family protein F:molecular_function unknown;P:response to auxin stimulus;C:cellular_component unknown;PO O.I. C.G. H.G.
18.0 99.5 17.9 At1g06980 837208 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
17.7 99.5 25.5 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.
17.6 99.5 215.6 At2g36320 818205 zinc finger (AN1-like) family protein F:DNA binding, zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MPOVF O.I. C.G. H.G.
17.5 99.5 51.8 At5g65910 836720 BSD domain-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB O.I. C.G. H.G.
17.0 99.5 58.4 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.
17.0 99.5 43.5 At3g20340 821578 - Expression of the gene is downregulated in the presence of paraquat, an inducer of photoxidative stress. O.I. C.G. H.G.
16.8 99.5 218.4 At1g80440 844383 kelch repeat-containing F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPBOFA O.I. C.G. H.G.
16.7 99.5 69.8 At1g76240 843957 unknown protein F:molecular_function unknown;P:unknown;C:chloroplast;PMO O.I. C.G. H.G.
16.7 99.5 64.4 At5g04530 830332 KCS19 (3-KETOACYL-COA SYNTHASE 19) Encodes KCS19, 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.
16.7 99.5 59.2 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.
16.7 99.5 42.2 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.
16.7 99.5 17.5 At4g12690 826881 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. C.G. H.G.
16.6 99.5 103.1 At3g45300 823668 IVD (ISOVALERYL-COA-DEHYDROGENASE) Encodes isovaleryl-coenzyme a dehydrogenase. O.I. C.G. H.G.
16.4 99.5 25.1 At5g67060 836841 HEC1 (HECATE 1) F:transcription factor activity;P:transmitting tissue development, carpel formation, regulation of transcription;C:nucleus;PMBOFA O.I. C.G. H.G.
16.3 99.5 134.8 At5g57655 835871 xylose isomerase family protein F:xylose isomerase activity;P:carbohydrate metabolic process;C:endoplasmic reticulum, plasma membrane, vacuole;BOPMF O.I. C.G. H.G.
16.3 99.5 62.5 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.
16.1 99.5 449.6 At4g20260 827773 DREPP plasma membrane polypeptide family protein Encodes a Ca2+ and Cu2+ binding protein. N-terminal myristylation on glycine 2 appears to enable it to associate tightly with the plasma membrane. Recombinant PCaP1 interacts strongly with phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) and PtdIns (3,4,5)P3, and weakly with PtdIns(3,5)P2 and PtdIns(4,5). It also interacts with calmodulin (CaM) in a calcium-dependent manner. CaM does not interfere with PCaP1 membrane localization but does weaken interactions between it and the PtdInsPs. PCaP1 has an apparent Kd of 10 uM for Cu2+ and can bind six ions per protein. Transcript levels for PCaP1 first fall and then rise following exposure to CuCl2. Mannitol, sorbitol, and the flg22 oligopeptide also increase expression levels. O.I. C.G. H.G.
16.1 99.5 289.4 At4g35750 829728 Rho-GTPase-activating protein-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO O.I. C.G. H.G.
16.1 99.5 42.4 At2g43060 818908 transcription factor F:transcription factor activity;P:regulation of transcription;C:nucleus;P O.I. C.G. H.G.
16.1 99.5 26.4 At3g52480 824413 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. C.G. H.G.
16.0 99.5 90.4 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.
16.0 99.5 30.7 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.
16.0 99.5 25.0 At4g16670 827369 phosphoinositide binding F:phosphoinositide binding;P:signal transduction;C:cellular_component unknown;PFO O.I. C.G. H.G.
15.8 99.5 109.9 At1g58180 842185 carbonic anhydrase family protein / carbonate dehydratase family protein F:carbonate dehydratase activity, zinc ion binding;P:carbon utilization;C:mitochondrion;BOPFMA O.I. C.G. H.G.
15.8 99.5 33.0 At4g36380 829790 ROT3 (ROTUNDIFOLIA 3) Encodes a cytochrome P-450 gene that is involved in leaf blade expansion by controlling polar cell expansion in the leaf length direction. Member of the CYP90C CYP450 family. ROT3 was shown to be involved in brassinosteroid biosynthesis, most likely in the conversion step of typhasterol (TY) to castasterone (CS). As 6-deoxo-CS was unable to restore the phenotype of rot3-1, it has been postulated that ROT3 might be specifically involved in the conversion of TY to CS in the C6-oxidation pathway of brassinolide. Recently, CYP90C1 was shown to catalyse the C-23 hydroxylation of several brassinosteroids (the enzyme has a broad specificity for 22-hydroxylated substrates). O.I. C.G. H.G.
15.7 99.5 206.7 At1g28330 839729 DYL1 (DORMANCY-ASSOCIATED PROTEIN-LIKE 1) dormancy-associated protein (DRM1) O.I. C.G. H.G.
15.7 99.5 77.9 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.
15.7 99.5 28.4 At1g09460 837469 glucan endo-1,3-beta-glucosidase-related F:unknown;P:unknown;C:endomembrane system;MPOBFVA O.I. C.G. H.G.
15.5 99.5 19.4 At1g21580 838759 hydroxyproline-rich glycoprotein family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFBVA O.I. C.G. H.G.
15.3 99.4 144.7 At5g66170 836749 - F:molecular_function unknown;P:aging;C:cellular_component unknown;PBOA 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.
62.6	99.8	159.6	At4g16515	827350	unknown protein	F:molecular_function unknown;P:unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
59.7	99.8	142.6	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.
55.8	99.8	306.6	At1g32170	840109	XTR4 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 4)	xyloglucan endotransglycosylase-related protein (XTR4)	O.I.	C.G.	H.G.
54.1	99.8	216.9	At4g37220	829876	stress-responsive protein, putative	F:molecular_function unknown;P:response to fructose stimulus, response to sucrose stimulus, response to glucose stimulus, response to stress;C:cellular_component unknown;P	O.I.	C.G.	H.G.
50.7	99.8	287.4	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.
40.8	99.8	170.5	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.
40.0	99.8	52.7	At4g23870	828486	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
37.1	99.7	131.2	At5g54190	835507	PORA	light-dependent NADPH:protochlorophyllide oxidoreductase A	O.I.	C.G.	H.G.
36.7	99.7	151.3	At5g02020	831782	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
35.1	99.7	367.7	At4g14130	827051	XTR7 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 7)	xyloglucan endotransglycosylase-related protein (XTR7)	O.I.	C.G.	H.G.
34.9	99.7	24.1	At1g52250		-	-	O.I.	C.G.	H.G.
34.0	99.7	93.3	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.
33.9	99.7	294.6	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.
33.0	99.7	103.0	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.
32.3	99.7	28.0	At1g29450	839821	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;P	O.I.	C.G.	H.G.
32.2	99.7	31.4	At2g45050	819112	zinc finger (GATA type) family protein	F:transcription factor activity;P:regulation of transcription, DNA-dependent;C:nucleus;FPMOV	O.I.	C.G.	H.G.
32.1	99.7	61.8	At5g18060	831310	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	C.G.	H.G.
31.9	99.7	289.0	At5g10430	830907	AGP4 (ARABINOGALACTAN PROTEIN 4)	Encodes arabinogalactan-protein (AGP4).	O.I.	C.G.	H.G.
31.5	99.7	120.7	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.
30.7	99.7	201.9	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.
30.6	99.7	373.9	At5g09440	830803	EXL4 (EXORDIUM LIKE 4)	F:molecular_function unknown;P:biological_process unknown;C:membrane;PB	O.I.	C.G.	H.G.
29.7	99.7	165.7	At3g06850	819869	BCE2	dihydrolipoamide branched chain acyltransferase	O.I.	C.G.	H.G.
28.2	99.7	24.2	At4g10910	826689	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
28.1	99.7	220.9	At5g60660	836187	PIP2	F:water channel activity;P:transport;C:integral to membrane, membrane;BPMOFAV	O.I.	C.G.	H.G.
28.1	99.7	35.8	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.
28.0	99.7	69.7	At1g02340	839300	HFR1 (LONG HYPOCOTYL IN FAR-RED)	Encodes a light-inducible, nuclear bHLH protein involved in phytochrome signaling. Mutants exhibit a long-hypocotyl phenotype only under far-red light but not under red light and are defective in other phytochrome A-related responses. Mutants also show blue light response defects. HFR1 interacts with COP1, co-localizes to the nuclear specks and is ubiquinated by COP1.	O.I.	C.G.	H.G.
27.6	99.7	62.0	At1g22740	838880	RABG3B	GTP-binding protein Rab7	O.I.	C.G.	H.G.
26.9	99.7	148.4	At2g44130	819019	kelch repeat-containing F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPBOFAV	O.I.	C.G.	H.G.
26.5	99.7	166.3	At1g12080	837760	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPVA	O.I.	C.G.	H.G.
26.2	99.7	16.7	At1g27670	839659	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
25.1	99.6	73.2	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.
25.0	99.6	349.7	At5g56870	835789	BGAL4 (beta-galactosidase 4)	F:beta-galactosidase activity;P:lactose catabolic process, using glucoside 3-dehydrogenase, carbohydrate metabolic process, lactose catabolic process via UDP-galactose, lactose catabolic process;C:endomembrane system, beta-galactosidase complex;PBMFOA	O.I.	C.G.	H.G.
24.3	99.6	394.2	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.
24.3	99.6	287.2	At3g61260	825298	DNA-binding family protein / remorin family protein	F:binding;P:biological_process unknown;C:plasma membrane, vacuole;OBMFPVA	O.I.	C.G.	H.G.
24.1	99.6	30.4	At4g39070	830062	zinc finger (B-box type) family protein	F:transcription factor activity, zinc ion binding;P:response to chitin, regulation of transcription;C:intracellular;POM	O.I.	C.G.	H.G.
23.9	99.6	416.4	At2g05540	815103	glycine-rich protein	F:unknown;P:unknown;C:endomembrane system;MPBOFVA	O.I.	C.G.	H.G.
23.1	99.6	19.6	At4g14380	827082	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;POM	O.I.	C.G.	H.G.
23.0	99.6	128.8	At2g34500	818013	CYP710A1 (cytochrome P450, family 710, subfamily A, polypeptide 1)	Encodes a protein with C22-sterol desaturase activity. The enzyme was shown to catalyze in the presence of NADPH the conversion of β-sitosterol to stigmasterol, but not that of 24-epi-campesterol to brassicasterol (unlike CYP710A2).	O.I.	C.G.	H.G.
22.8	99.6	106.8	At1g67910	843119	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;P	O.I.	C.G.	H.G.
22.7	99.6	270.7	At3g23050	821879	IAA7 (INDOLE-3-ACETIC ACID 7)	Transcription regulator acting as repressor of auxin-inducible gene expression. Plays role in the control of gravitropic growth and development in light-grown seedlings. Auxin induces the degradation of the protein in a dosage-dependent manner in a process mediated by AtRac1. Auxin induced the relocalization of the protein within the nucleus from a diffused nucleoplasmic pattern to a discrete particulated pattern named nuclear protein bodies or NPB in a process also mediated by Rac1. Colocalizes with SCF, CSN and 26S proteasome components.	O.I.	C.G.	H.G.
22.6	99.6	247.2	At3g26510	822258	octicosapeptide/Phox/Bem1p (PB1) domain-containing protein	F:unknown;P:biological_process unknown;C:unknown;POFMBV	O.I.	C.G.	H.G.
22.4	99.6	244.0	At5g65390	836664	AGP7	F:unknown;P:unknown;C:anchored to membrane;BMOPFVA	O.I.	C.G.	H.G.
22.3	99.6	70.9	At2g28110	817357	FRA8 (FRAGILE FIBER 8)	Homolog to AT5G22940, a member of glycosyltransferase family 47 that is involved in secondary cell wall biosynthesis. It exhibits high sequence similarity to tobacco (Nicotiana plumbaginifolia) pectin glucuronyltransferase. Protein has a domain that shares significant similarity with the pfam03016 domain. It is expressed specifically in developing vessels and fiber cells, and FRA8 is targeted to Golgi. Mutants have irregular xylem formation, reduced cellulose levels and plants are smaller than normal siblings.	O.I.	C.G.	H.G.
22.2	99.6	176.8	At2g17710	816280	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
22.1	99.6	153.7	At1g10070	837543	ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2)	Encodes a chloroplast branched-chain amino acid aminotransferase. Complements the yeast leu/iso-leu/val auxotrophy mutant.	O.I.	C.G.	H.G.
21.8	99.6	73.2	At3g05900	819759	neurofilament protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAV	O.I.	C.G.	H.G.
21.6	99.6	179.1	At3g52060	824369	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POB	O.I.	C.G.	H.G.
21.3	99.6	51.1	At2g28200	817366	nucleic acid binding / transcription factor/ zinc ion binding	F:transcription factor activity, zinc ion binding, nucleic acid binding;P:regulation of transcription;C:intracellular;MPOF	O.I.	C.G.	H.G.
21.2	99.6	151.5	At1g03090	838362	MCCA	MCCA is the biotinylated subunit of the dimer MCCase, which is involved in leucine degradation. Both subunits are nuclear coded and the active enzyme is located in the mitochondrion.	O.I.	C.G.	H.G.
21.0	99.6	86.4	At4g28270	828942	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;MPFOV	O.I.	C.G.	H.G.
21.0	99.6	69.9	At3g49790	824141	ATP binding	F:ATP binding;P:biological_process unknown;C:unknown;P	O.I.	C.G.	H.G.
20.8	99.6	27.1	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.
20.4	99.6	212.6	At1g08510	837372	FATB (fatty acyl-ACP thioesterases B)	Encodes an acyl-acyl carrier protein thioesterase. Hydrolyzes primarily saturated acyl-ACPs with chain lengths that vary between 8 and 18 carbons. Involved in saturated fatty acid synthesis. Nuclear-encoded, plastid-targeted globular protein that is functional as dimer.	O.I.	C.G.	H.G.
20.4	99.6	116.1	At1g64660	842774	ATMGL (ARABIDOPSIS THALIANA METHIONINE GAMMA-LYASE)	Encodes a functional methionine gamma-lyase, a cytosolic enzyme catalyzes the degradation of methionine into methanethiol, alpha-ketobutyrate and ammonia. The catabolism of excess methionine is important to methionine homeostasis.	O.I.	C.G.	H.G.
20.3	99.6	41.4	At1g29500	839827	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:nucleolus, nucleus;P	O.I.	C.G.	H.G.
20.1	99.6	82.3	At3g29575	822619	AFP3 (ABI FIVE BINDING PROTEIN 3)	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POM	O.I.	C.G.	H.G.
20.1	99.6	15.7	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.
19.8	99.6	16.9	At4g36900	829843	RAP2.10 (related to AP2 10)	encodes a member of the DREB subfamily A-5 of ERF/AP2 transcription factor family (RAP2.10). The protein contains one AP2 domain. There are 16 members in this subfamily including RAP2.9 and RAP2.1.	O.I.	C.G.	H.G.
19.7	99.6	179.3	At3g61060	825278	AtPP2-A13 (Arabidopsis thaliana phloem protein 2-A13)	F:carbohydrate binding;P:N-terminal protein myristoylation, response to wounding;C:unknown;P	O.I.	C.G.	H.G.
19.5	99.6	208.5	At5g53250	835406	AGP22 (ARABINOGALACTAN PROTEIN 22)	F:unknown;P:unknown;C:anchored to membrane;P	O.I.	C.G.	H.G.
19.5	99.6	201.6	At5g18650	831983	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFA	O.I.	C.G.	H.G.
19.3	99.6	14.4	At1g21360	838735	GLTP2 (glycolipid transfer protein 2)	F:glycolipid transporter activity, glycolipid binding;P:glycolipid transport;C:cytoplasm;P	O.I.	C.G.	H.G.
19.2	99.6	75.4	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.
19.1	99.6	192.3	At1g04250	839568	AXR3 (AUXIN RESISTANT 3)	Transcription regulator acting as repressor of auxin-inducible gene expression. Auxin-inducible AUX/IAA gene. Short-lived nuclear protein with four conserved domains. Domain III has homology to beta alpha alpha dimerization and DNA binding domains. Involved in auxin signaling. Auxin induces the degradation of the protein in a dosage-dependent manner in a process mediated by AtRac1. Auxin induced the relocalization of the protein within the nucleus from a diffused nucleoplasmic pattern to a discrete particulated pattern named nuclear protein bodies or NPB in a process also mediated by Rac1. Colocalizes with SCF, CSN and 26S proteasome components.	O.I.	C.G.	H.G.
19.0	99.5	34.6	At2g41850	818785	PGAZAT (POLYGALACTURONASE ABSCISSION ZONE A. THALIANA)	ADPG2.	O.I.	C.G.	H.G.
18.9	99.5	35.6	At3g59690	825138	IQD13 (IQ-domain 13)	F:calmodulin binding;P:unknown;C:plasma membrane;POMVFB	O.I.	C.G.	H.G.
18.7	99.5	202.9	At2g21140	816649	ATPRP2 (PROLINE-RICH PROTEIN 2)	Proline-rich protein expressed in expanding leaves, stems, flowers, and siliques.	O.I.	C.G.	H.G.
18.6	99.5	55.5	At1g02860	839559	NLA (nitrogen limitation adaptation)	Encodes a likely ubiquitin E3 ligase with RING and SPX domains that is involved in mediating immune responses.	O.I.	C.G.	H.G.
18.6	99.5	33.7	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.
18.1	99.5	96.1	At4g34760	829628	auxin-responsive family protein	F:molecular_function unknown;P:response to auxin stimulus;C:cellular_component unknown;PO	O.I.	C.G.	H.G.
18.0	99.5	17.9	At1g06980	837208	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
17.7	99.5	25.5	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.
17.6	99.5	215.6	At2g36320	818205	zinc finger (AN1-like) family protein	F:DNA binding, zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MPOVF	O.I.	C.G.	H.G.
17.5	99.5	51.8	At5g65910	836720	BSD domain-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFB	O.I.	C.G.	H.G.
17.0	99.5	58.4	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.
17.0	99.5	43.5	At3g20340	821578	-	Expression of the gene is downregulated in the presence of paraquat, an inducer of photoxidative stress.	O.I.	C.G.	H.G.
16.8	99.5	218.4	At1g80440	844383	kelch repeat-containing F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPBOFA	O.I.	C.G.	H.G.
16.7	99.5	69.8	At1g76240	843957	unknown protein	F:molecular_function unknown;P:unknown;C:chloroplast;PMO	O.I.	C.G.	H.G.
16.7	99.5	64.4	At5g04530	830332	KCS19 (3-KETOACYL-COA SYNTHASE 19)	Encodes KCS19, 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.
16.7	99.5	59.2	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.
16.7	99.5	42.2	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.
16.7	99.5	17.5	At4g12690	826881	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	C.G.	H.G.
16.6	99.5	103.1	At3g45300	823668	IVD (ISOVALERYL-COA-DEHYDROGENASE)	Encodes isovaleryl-coenzyme a dehydrogenase.	O.I.	C.G.	H.G.
16.4	99.5	25.1	At5g67060	836841	HEC1 (HECATE 1)	F:transcription factor activity;P:transmitting tissue development, carpel formation, regulation of transcription;C:nucleus;PMBOFA	O.I.	C.G.	H.G.
16.3	99.5	134.8	At5g57655	835871	xylose isomerase family protein	F:xylose isomerase activity;P:carbohydrate metabolic process;C:endoplasmic reticulum, plasma membrane, vacuole;BOPMF	O.I.	C.G.	H.G.
16.3	99.5	62.5	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.
16.1	99.5	449.6	At4g20260	827773	DREPP plasma membrane polypeptide family protein	Encodes a Ca2+ and Cu2+ binding protein. N-terminal myristylation on glycine 2 appears to enable it to associate tightly with the plasma membrane. Recombinant PCaP1 interacts strongly with phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) and PtdIns (3,4,5)P3, and weakly with PtdIns(3,5)P2 and PtdIns(4,5). It also interacts with calmodulin (CaM) in a calcium-dependent manner. CaM does not interfere with PCaP1 membrane localization but does weaken interactions between it and the PtdInsPs. PCaP1 has an apparent Kd of 10 uM for Cu2+ and can bind six ions per protein. Transcript levels for PCaP1 first fall and then rise following exposure to CuCl2. Mannitol, sorbitol, and the flg22 oligopeptide also increase expression levels.	O.I.	C.G.	H.G.
16.1	99.5	289.4	At4g35750	829728	Rho-GTPase-activating protein-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPO	O.I.	C.G.	H.G.
16.1	99.5	42.4	At2g43060	818908	transcription factor	F:transcription factor activity;P:regulation of transcription;C:nucleus;P	O.I.	C.G.	H.G.
16.1	99.5	26.4	At3g52480	824413	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	C.G.	H.G.
16.0	99.5	90.4	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.
16.0	99.5	30.7	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.
16.0	99.5	25.0	At4g16670	827369	phosphoinositide binding	F:phosphoinositide binding;P:signal transduction;C:cellular_component unknown;PFO	O.I.	C.G.	H.G.
15.8	99.5	109.9	At1g58180	842185	carbonic anhydrase family protein / carbonate dehydratase family protein	F:carbonate dehydratase activity, zinc ion binding;P:carbon utilization;C:mitochondrion;BOPFMA	O.I.	C.G.	H.G.
15.8	99.5	33.0	At4g36380	829790	ROT3 (ROTUNDIFOLIA 3)	Encodes a cytochrome P-450 gene that is involved in leaf blade expansion by controlling polar cell expansion in the leaf length direction. Member of the CYP90C CYP450 family. ROT3 was shown to be involved in brassinosteroid biosynthesis, most likely in the conversion step of typhasterol (TY) to castasterone (CS). As 6-deoxo-CS was unable to restore the phenotype of rot3-1, it has been postulated that ROT3 might be specifically involved in the conversion of TY to CS in the C6-oxidation pathway of brassinolide. Recently, CYP90C1 was shown to catalyse the C-23 hydroxylation of several brassinosteroids (the enzyme has a broad specificity for 22-hydroxylated substrates).	O.I.	C.G.	H.G.
15.7	99.5	206.7	At1g28330	839729	DYL1 (DORMANCY-ASSOCIATED PROTEIN-LIKE 1)	dormancy-associated protein (DRM1)	O.I.	C.G.	H.G.
15.7	99.5	77.9	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.
15.7	99.5	28.4	At1g09460	837469	glucan endo-1,3-beta-glucosidase-related	F:unknown;P:unknown;C:endomembrane system;MPOBFVA	O.I.	C.G.	H.G.
15.5	99.5	19.4	At1g21580	838759	hydroxyproline-rich glycoprotein family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFBVA	O.I.	C.G.	H.G.
15.3	99.4	144.7	At5g66170	836749	-	F:molecular_function unknown;P:aging;C:cellular_component unknown;PBOA	O.I.	C.G.	H.G.

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GSM ID	GSM292076
Assay name	Wt, dark sample, biological rep1
GSE experiment	GSE11594: Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings

Microarray experiments to specifically-expressed genes

GSM ID GSM292076 Assay name Wt, dark sample, biological rep1 GSE experiment GSE11594: Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings

GSM ID GSM292076

Assay name Wt, dark sample, biological rep1

GSE experiment GSE11594: Expression data from dark grown Arabidopsis Wild type (Wt, col-o) and pif1-2 (At2g20810, Salk_072677) mutant seedlings