Microarray experiments to specifically-expressed genes

GSM ID GSM245910
Assay name csn3-1 mutant light replicate 1
GSE experiment GSE9728: COP9 signalosome (csn) mutant analysis

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
140.499.972.2At4g21070827854ATBRCA1Encodes AtBRCA1, an ortholog of the human breast cancer susceptibility gene 1. Contains one N-terminal RING finger, two C-terminal BRCT and the p300/CBP interacting domain. Strongly induced by gamma rays, consistent with a putative role in DNA repair and in cell cycle control.O.I.C.G.H.G.
85.699.9553.0At4g12490826861protease inhibitor/seed storage/lipid transfer protein (LTP) family proteinF:lipid binding;P:defense response to fungus, lipid transport;C:unknown;PBOMVFAO.I.C.G.H.G.
83.799.930.5At4g19130827651DNA binding / nucleic acid binding / zinc ion bindingF:DNA binding, zinc ion binding, nucleic acid binding;P:DNA replication;C:nucleus;MPOFAO.I.C.G.H.G.
51.899.824.9At4g29170829038ATMND1A homolog of yeast, mouse and human mnd1delta protein. Null mutants exhibit normal vegetative and flower development; however, during prophase I, chromosomes become fragmented resulting in random distribution of the fragments between polyads. Both male and female meiosis are defective and strong accumulation of AtRAD51 was observed in the inflorescence nuclei of mutant plants. Similarly to its yeast and animal homologues, AtMnd1 might play a role in DSB repair during meiosis.O.I.C.G.H.G.
45.899.891.7At5g49160834975MET1 (METHYLTRANSFERASE 1)Encodes a cytosine methyltransferase MET1. Required for silencing of FWA paternal allele in endosperm. Two lines with RNAi constructs directed against DMT1 have reduced agrobacterium-mediated tumor formation.O.I.C.G.H.G.
44.899.8104.7At1g57820842157VIM1 (VARIANT IN METHYLATION 1)Encodes a 645-amino acid methylcytosine-binding protein with a PHD domain, two RING finger domains, and an SRA domain that is involved in centromere heterochromatinization. This protein functions as an E3 ubiquitin ligase in vitro. The protein has been shown to bind to methylated cytosines of CG, CNG and CNN motifs via its SRA domain but has a preference for the former. It plays a role in the establishment/maintenance of chromatin structure during cell division and is localized in the nucleus. Plants over-expressing VIM1/ORTH2 show an inhibition in root growth and a delay in flowering. Both over-expression of GFP:ORTH2 and loss of ORTH2/VIM1 lead to decreased levels of DNA methylation. GFP:ORTH2 over-expressers also have increased levels of FWA transcripts.O.I.C.G.H.G.
42.599.8162.0At1g76930844028ATEXT4 (EXTENSIN 4)Encodes an Arabidopsis extensin gene that belongs to cell-wall hydroxyproline-rich glycoproteins. The cross-link of extensins enforces cell wall strength. Transgenic plants overexpressing this gene show an increase in stem thickness.O.I.C.G.H.G.
40.199.8419.1At3g27060822324TSO2 (TSO meaning 'ugly' in Chinese)Encodes one of the 3 ribonucleotide reductase (RNR) small subunit genes. TSO2 transcription occurs predominantly at the S-phase of the cell cycle and its expression pattern is consistent with its role in dNDP biosynthesis during DNA replication in actively dividing cells. Critical for cell cycle progression, DNA damage repair and plant development.O.I.C.G.H.G.
39.999.8142.8At1g65500842862unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.C.G.H.G.
37.999.8391.7At4g14690827119ELIP2 (EARLY LIGHT-INDUCIBLE PROTEIN 2)Encodes an early light-induced protein. ELIPs are thought not to be directly involved in the synthesis and assembly of specific photosynthetic complexes, but rather affect the biogenesis of all chlorophyll-binding complexes. A study (PMID 17553115) has shown that the chlorophyll synthesis pathway was downregulated as a result of constitutive ELIP2 expression, leading to decreased chlorophyll availability for the assembly of pigment-binding proteins for photosynthesis.O.I.C.G.H.G.
34.699.734.5At1g17960838375threonyl-tRNA synthetase, putative / threonine--tRNA ligase, putativeF:nucleotide binding, aminoacyl-tRNA ligase activity, threonine-tRNA ligase activity, ATP binding;P:threonyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:cytoplasm;BOMFAPO.I.C.G.H.G.
32.699.720.4At1g67180843038zinc finger (C3HC4-type RING finger) family protein / BRCT domain-containing proteinF:protein binding, zinc ion binding;P:unknown;C:intracellular;MOFPVO.I.C.G.H.G.
30.999.749.9At4g02390828049APP (ARABIDOPSIS POLY(ADP-RIBOSE) POLYMERASE)Encodes a DNA dependent nuclear poly (ADP-ribose) polymerase (E.C.2.4.2.30), thought to be involved in post-translational modification .O.I.C.G.H.G.
27.699.724.8At5g02220831792unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
26.899.7140.0At3g07800819971thymidine kinase, putativeF:thymidine kinase activity, ATP binding;P:pyrimidine deoxyribonucleoside interconversion, anaerobic respiration;C:cellular_component unknown;BOVMPAFO.I.C.G.H.G.
24.599.679.8At3g54750824640unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.C.G.H.G.
24.299.6282.1At4g12480826860pEARLI 1a putative lipid transfer protein, vernalization-responsive and cold-inducedO.I.C.G.H.G.
23.299.6107.6At1g14720838037XTR2 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE RELATED 2)member of Glycoside Hydrolase Family 16O.I.C.G.H.G.
23.199.619.6At5g38780833869S-adenosyl-L-methionine:carboxyl methyltransferase family proteinF:S-adenosylmethionine-dependent methyltransferase activity, methyltransferase activity;P:biological_process unknown;C:cellular_component unknown;POBMFO.I.C.G.H.G.
21.399.6174.5At2g36910818265ABCB1 (ATP BINDING CASSETTE SUBFAMILY B1)Belongs to the family of ATP-binding cassette (ABC) transporters. Also known as AtMDR1.Possibly regulates auxin-dependent responses by influencing basipetal auxin transport in the root. Exerts nonredundant, partially overlapping functions with the ABC transporter encoded by AT3G28860. PGP1 mediates cellular efflux of IAA and interacts with PIN genes that may confer an accelerated vectoral component to PGP-mediated transport. The non-polar localization of PGP1 at root and shoot apices, where IAA gradient-driven transport is impaired, may be required to confer directionality to auxin transport in those tissues.O.I.C.G.H.G.
19.899.643.2At1g33560840250ADR1 (ACTIVATED DISEASE RESISTANCE 1)Encodes a NBS-LRR disease resistance protein that possesses N-terminal kinase subdomains. Activation tagged mutant of ADR1 showed elevated levels of SA and reactive oxygen species in addition to number of defense gene transcripts. Exhibits resistance to number of microbial pathogens.O.I.C.G.H.G.
19.699.6232.8At2g43510818952ATTI1Member of the defensin-like (DEFL) family. Encodes putative trypsin inhibitor protein which may function in defense against herbivory.O.I.C.G.H.G.
18.599.5106.2At2g21790816715RNR1 (RIBONUCLEOTIDE REDUCTASE 1)encodes large subunit of ribonucleotide reductase involved in the production of deoxyribonucleoside triphosphates (dNTPs) for DNA replication and repairO.I.C.G.H.G.
17.699.541.4At5g48720834930XRI1 (X-RAY INDUCED TRANSCRIPT 1)Encodes XRI1 (X-ray induced 1). Required for post-meiotic stages of pollen development and male and female meiosis. Maybe required for meiotic DNA repair. Inducible by X-ray. Homozygous xri1 mutants are sterile due to extensive chromosome fragmentation.O.I.C.G.H.G.
16.799.540.4At1g57770842152amine oxidase familyF:oxidoreductase activity;P:unknown;C:chloroplast;OBMPAFO.I.C.G.H.G.
16.399.519.6At2g18600816375RUB1-conjugating enzyme, putativeF:ubiquitin-protein ligase activity, small conjugating protein ligase activity, acid-amino acid ligase activity, ATP binding;P:regulation of protein metabolic process, protein modification process, post-translational protein modification;C:cellular_component unknown;MFOPVO.I.C.G.H.G.
16.299.533.0At1g66040842917VIM4 (VARIANT IN METHYLATION 4)predicted to encode a protein with an N-terminal PHD domain and two RING domains surrounding an SRA domain. Attempts to isolate ORTH4/VIM4 cDNA through RT-PCR were unsuccessful and analysis of the expression of this gene is difficult since it shares 99% nucleotide identity with ORTH5/VIM2.O.I.C.G.H.G.
16.199.57.3At1g45616841101AtRLP6 (Receptor Like Protein 6)F:protein binding;P:signal transduction, defense response;C:membrane;PMOBFAVO.I.C.G.H.G.
14.099.424.9At4g139003770199-F:unknown;P:unknown;C:unknownO.I.C.G.H.G.
13.999.4229.3At4g15910827273ATDI21 (ARABIDOPSIS THALIANA DROUGHT-INDUCED 21)encodes a gene whose transcript level in root and leaves increases to progressive drought stress. The transcript level is also affected by changes of endogenous or exogenous abscisic acid level. It appears to be a member of plant-specific gene family that includes late embryo-abundant and zinc- IAA-induced proteins in other plants.O.I.C.G.H.G.
13.399.4202.1At3g18280821356protease inhibitor/seed storage/lipid transfer protein (LTP) family proteinF:lipid binding;P:lipid transport;C:endomembrane system;PO.I.C.G.H.G.
13.299.434.5At1g15660838135CENP-C (CENTROMERE PROTEIN C)Encodes a homologue of the human centromeric protein C (CENP-C). CENP-C co-localizes with the 180 bp centromeric regions of chromosomes throughout the cell cycle, but does not completely cover the 180 bp regions.O.I.C.G.H.G.
11.899.340.1At5g61000836221replication protein, putativeF:DNA binding, nucleic acid binding;P:DNA replication;C:nucleus;PMOFAO.I.C.G.H.G.
11.499.3393.6At4g12470826859protease inhibitor/seed storage/lipid transfer protein (LTP) family proteinF:lipid binding;P:defense response to fungus, lipid transport;C:endomembrane system;PBOVMFAO.I.C.G.H.G.
11.399.330.4At4g23260828425ATP binding / protein kinase/ protein serine/threonine kinase/ protein tyrosine kinaseF:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:response to abscisic acid stimulus;C:endomembrane system;MPOBFVAO.I.C.G.H.G.
11.299.2296.0At4g34710829623ADC2 (ARGININE DECARBOXYLASE 2)encodes a arginine decarboxylase (ADC), a rate-limiting enzyme that catalyzes the first step of polyamine (PA) biosynthesis via ADC pathway in Arabidopsis thaliana. Arabidopsis genome has two ADC paralogs, ADC1 and ADC2. ADC2 is stress-inducible (osmotic stress). Double mutant analysis showed that ADC genes are essential for the production of PA, and are required for normal seed development. Overexpression causes phenotypes similar to GA-deficient plants and these plants show reduced levels of GA due to lower expression levels of AtGA20ox1, AtGA3ox3 and AtGA3ox1.O.I.C.G.H.G.
11.299.250.2At3g61960825369protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOFBVAO.I.C.G.H.G.
11.099.226.8At5g18270831945ANAC087F:transcription factor activity;P:multicellular organismal development, regulation of transcription;C:cellular_component unknown;PO.I.C.G.H.G.
10.899.212.8At5g17890831657DAR4 (DA1-RELATED PROTEIN 4)F:protein binding, zinc ion binding, ATP binding;P:defense response, apoptosis;C:unknown;PMOFBVAO.I.C.G.H.G.
10.799.2438.6At3g49110824072PRXCA (PEROXIDASE CA)Class III peroxidase Perx33. Expressed in roots. Located in the cell wall. Involved in cell elongation. Expression activated by light. May play a role in generating H2O2 during defense response.O.I.C.G.H.G.
10.799.210.3At1g67370843058ASY1 (ASYNAPTIC 1)meiotic asynaptic mutant 1 (ASY1). ASY1 protein is initially distributed as numerous foci throughout the chromatin. During early G2, the foci are juxtaposed to the nascent chromosome axes to form a continuous axis associated signal.O.I.C.G.H.G.
10.399.221.8At3g45730823715unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.C.G.H.G.
9.999.139.7At4g23290828428protein kinase family proteinF:kinase activity;P:protein amino acid phosphorylation;C:mitochondrion;MPOBFVAO.I.C.G.H.G.
9.999.19.9At3g20710821619F-box protein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.C.G.H.G.
9.899.115.5At1g31280840016AGO2 (argonaute 2)An Argonaute geneO.I.C.G.H.G.
9.499.1442.0At3g22120821775CWLP (CELL WALL-PLASMA MEMBRANE LINKER PROTEIN)cell wall-plasma membrane linker protein homolog (CWLP)O.I.C.G.H.G.
9.499.1315.1At2g254508170832-oxoglutarate-dependent dioxygenase, putativeencodes a protein whose sequence is similar to ACC oxidaseO.I.C.G.H.G.
9.499.136.4At3g28540822484AAA-type ATPase family proteinF:nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;P:unknown;C:unknown;BOMFPAVO.I.C.G.H.G.
9.399.119.9At2g32590817819-F:unknown;P:mitosis, mitotic cell cycle;C:nucleus, chloroplast;MFOPVO.I.C.G.H.G.
9.399.17.6At2g18120816325SRS4 (SHI-RELATED SEQUENCE 4)A member of SHI gene family. Arabidopsis thaliana has ten members that encode proteins with a RING finger-like zinc finger motif. Despite being highly divergent in sequence, many of the SHI-related genes are partially redundant in function and synergistically promote gynoecium, stamen and leaf development in Arabidopsis.O.I.C.G.H.G.
9.199.1898.3At2g25510817089unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.C.G.H.G.
9.199.120.7At4g23300828429protein kinase family proteinF:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.C.G.H.G.
9.199.116.9At1g33720840263CYP76C6member of CYP76CO.I.C.G.H.G.
9.199.113.1At3g20490821595unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBPO.I.C.G.H.G.
9.199.17.8At5g45400834576replication protein, putativeF:DNA binding, zinc ion binding, nucleic acid binding;P:DNA replication;C:nucleus;MPFOABO.I.C.G.H.G.
9.099.172.4At4g23140828413CRK6 (CYSTEINE-RICH RLK 6)Arabidopsis thaliana receptor-like protein kinase. Naming convention from Chen et al 2003 (PMID 14756307)O.I.C.G.H.G.
8.999.052.0At2g41230818722unknown proteinF:unknown;P:biological_process unknown;C:unknown;PMO.I.C.G.H.G.
8.899.0144.4At5g08040830698TOM5 (MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM5 HOMOLOG)F:molecular_function unknown;P:biological_process unknown;C:mitochondrion, plastid;PO.I.C.G.H.G.
8.899.039.6At1g69770843313CMT3 (chromomethylase 3)Encodes a chromomethylase involved in methylating cytosine residues at non-CG sites. Involved in preferentially methylating transposon-related sequences, reducing their mobility. CMT3 interacts with an Arabidopsis homologue of HP1 (heterochromatin protein 1), which in turn interacts with methylated histones. Involved in gene silencing.O.I.C.G.H.G.
8.799.020.2At1g04020839329BARD1 (BREAST CANCER ASSOCIATED RING 1)Encodes a protein containing two tandem BRCA1 C-Terminal (BRCT) domains, which function in phosphorylation-dependent protein–protein interactions.Loss of function mutations cause defects in meristem organization due to failure to repress WUS. BARD1 binds to WUS promoter and over expression of BARD reduces the extent of WUS expression.O.I.C.G.H.G.



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