Co-expression analysis

Gene ID At1g59580
Gene name ATMPK2 (ARABIDOPSIS THALIANA MITOGEN-ACTIVATED PROTEIN KINASE HOMOLOG 2)
Module size 54 genes
NF 0.43
%ile 61.0



Co-expression network

pink confeito: Transcription factor, green bicone: Binding protein, red cone: Enzyme protein, blue sphere: Other protein
large node: VF over 0.50, middle node: over 0.25, small node: below 0.25



Co-expressed genes

Click gene/probe ID to show a list of genes that are co-expressed with the gene.

VF %ile CC Gene ID Repr. ID Gene name Func. O.I. H.G. S.X. Other DB
0.8391.41.00At1g59580842248ATMPK2 (ARABIDOPSIS THALIANA MITOGEN-ACTIVATED PROTEIN KINASE HOMOLOG 2)encodes a mitogen-activated kinase involved in innate immunityO.I.H.G.S.X.
0.7687.40.94At5g22360832297ATVAMP714 (VESICLE-ASSOCIATED MEMBRANE PROTEIN 714)Member of Synaptobrevin-like AtVAMP7C, v-SNARE protein family.O.I.H.G.S.X.
0.6478.90.93At2g15570816050thioredoxin M-type 3, chloroplast (TRX-M3)chloroplast protein similar to prokaryotic thioredoxin.O.I.H.G.S.X.
0.6277.30.93At3g04880819648DRT102 (DNA-DAMAGE-REPAIR/TOLERATION 2)encodes a novel protein involved in DNA repair from UV damage. Isolated by functional complementation of E. coli UV-sensitive mutants (UVR genes).O.I.H.G.S.X.
0.6176.70.92At3g30390822740amino acid transporter family proteinEncodes a putative amino acid transporter.O.I.H.G.S.X.
0.6176.70.92At5g10960830963CCR4-NOT transcription complex protein, putativeF:ribonuclease activity, nucleic acid binding;P:RNA modification;C:nucleus;PMOFO.I.H.G.S.X.
0.5974.70.92At5g18120831930ATAPRL7 (APR-like 7)Encodes a protein disulfide isomerase-like (PDIL) protein, a member of a multigene family within the thioredoxin (TRX) superfamily. This protein also belongs to the adenosine 5'-phosphosulfate reductase-like (APRL) group.O.I.H.G.S.X.
0.5673.00.91At1g79590844297SYP52 (SYNTAXIN OF PLANTS 52)Encodes one of 24 Arabidopsis syntaxins. Its mRNA has been shown to be expressed.O.I.H.G.S.X.
0.5570.60.92At1g17080838278unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.5570.60.92At5g65430836668GRF8 (GENERAL REGULATORY FACTOR 8)member of 14-3-3 proteins. This protein is reported to interact with the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1O.I.H.G.S.X.
0.5469.50.92At5g46860834730VAM3Syntaxin-related protein required for vacuolar assembly. A member of t-SNARE superfamily, homologous to yest Vam3p. Localized in the vacuolar membranes. The protein has a heptad repeat structure (residues164220) in which hydrophobic amino acid residues appear at seven amino acid intervals. Such regions have a high potential to form an amphiphilic a-helix, intriguing for the intermolecular interactions by forming coiled-coil structure. AtVam3p has a highly hydrophobic segment at its C terminus thus implicating it to be a membrane protein while the rest of the sequence is hydrophilic.O.I.H.G.S.X.
0.5368.60.92At2g32080817768PUR ALPHA-1similar to the conserved animal nuclear protein PUR alpha which was implicated in the control of gene transcription and DNA replicationO.I.H.G.S.X.
0.5368.60.92At3g47670823921enzyme inhibitor/ pectinesterase/ pectinesterase inhibitorF:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.5267.40.92At5g27840832846TOPP8encodes a serine/threonine protein phosphatase expressed in expressed in roots, rosettes and flowers.O.I.H.G.S.X.
0.5065.30.93At4g28770828998-F:molecular_function unknown;P:unknown;C:plasma membrane, vacuole, membrane;POO.I.H.G.S.X.
0.4963.50.91At5g10860830953CBS domain-containing proteinF:unknown;P:response to salt stress;C:mitochondrion;BOAPFMO.I.H.G.S.X.
0.4963.50.91At2g45980819206unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.4963.50.91At2g28370817385-F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;PO.I.H.G.S.X.
0.4963.50.91At1g01550839536BPS1 (BYPASS 1)BYPASS1, required to prevent constitutive production of a root-derived graft-transmissible signalO.I.H.G.S.X.
0.4862.50.92At3g55770824743LIM domain-containing proteinF:zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MOPFO.I.H.G.S.X.
0.4862.50.92At4g13270826957unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO.I.H.G.S.X.
0.4761.20.92At1g76920844027F-box family protein (FBX3)F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:unknown;PO.I.H.G.S.X.
0.4659.80.92At1g16180838187TMS membrane family protein / tumour differentially expressed (TDE) family proteinF:molecular_function unknown;P:unknown;C:endomembrane system, membrane;MFPOO.I.H.G.S.X.
0.4558.30.92At4g02080827368ATSAR2 (ARABIDOPSIS THALIANA SECRETION-ASSOCIATED RAS SUPER FAMILY 2)A member of ARF-like GTPase family. A thaliana has 21 members, in two subfamilies, ARF and ARF-like (ARL) GTPases.O.I.H.G.S.X.
0.4558.30.91At3g11530820326vacuolar protein sorting 55 family protein / VPS55 family proteinF:transporter activity;P:transport;C:vacuole;FMPOO.I.H.G.S.X.
0.4558.30.91At5g20650832188COPT5encodes a member of copper transporter family and functionally complements a high affinity copper transporter mutant in yeastO.I.H.G.S.X.
0.4558.30.92At1g64040842708TOPP3Encodes the catalytic subunit of a Type 1 phosphoprotein Ser/Thr phosphatase, expressed in roots, shoots and flowers.O.I.H.G.S.X.
0.4355.30.91At5g10450830909GRF6 (G-box regulating factor 6)Encodes a member of the 14-3-3 gene family that is a lambda isoform (14-3-3λ). Interacts with APX3 (ascorbate peroxidase) and AKR2 , suggesting a role in mediating oxidative metabolism in stress response. This protein was shown to colocalize and interact with SERK1 by which it is phosphorylated. This protein is also reported to interact with the phosphorylated form of the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1.O.I.H.G.S.X.
0.4253.90.92At4g22750828372zinc finger (DHHC type) family proteinF:zinc ion binding;P:unknown;C:endomembrane system;MOFPO.I.H.G.S.X.
0.4050.80.91At1g73030843634VPS46.2F:unknown;P:vesicle-mediated transport;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.3948.40.91At5g58060835918YKT61member of YKT6 Gene FamilyO.I.H.G.S.X.
0.3948.40.91At2g23780816910zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFVO.I.H.G.S.X.
0.3846.70.91At3g03860821101ATAPRL5 (APR-like 5)Encodes a protein disulfide isomerase-like (PDIL) protein, a member of a multigene family within the thioredoxin (TRX) superfamily. This protein also belongs to the adenosine 5'-phosphosulfate reductase-like (APRL) group.O.I.H.G.S.X.
0.3846.70.92At5g39510833947SGR4 (SHOOT GRAVITROPSIM 4)Encodes a member of SNARE gene family. Homologous with yeast VTI1 and is involved in vesicle transport. Mutant alleles such as sgr4/zig are defective in the shoots response to gravity resulting in a zigzag growth pattern of the stem. Involved in protein trafficking to lytic vacuoles. Can conditionally substitute VTI12 in protein storage vacuole trafficking when plants are devoid of VTI12.O.I.H.G.S.X.
0.3846.70.92At1g03900839378ATNAP4 (Arabidopsis thaliana non-intrinsic ABC protein 4)member of NAP family, an heterogeneous subfamily of the ATP-binding Cassette (ABC) superfamily of membrane transporters. The NAPs proteins are characterized by having only one nucleotide-binding folds (NBFs) domain.O.I.H.G.S.X.
0.3745.00.91At3g62290825402ATARFA1E (ADP-ribosylation factor A1E)A member of ARF GTPase family. A thaliana has 21 members of this family, known to be essential for vesicle coating and uncoating and functions in GTP-binding. The gene is shown to play a role in cell division, cell expansion and cellulose production using antisense construct.O.I.H.G.S.X.
0.3745.00.92At5g63910836512FCLY (FARNESYLCYSTEINE LYASE)encodes for a farnesylcysteine lyase (EC 1.8.3.5 - prenylcysteine oxidase) involved in a salvage pathway of farnesyl diphosphate.O.I.H.G.S.X.
0.3745.00.92At4g39910830150ATUBP3 (ARABIDOPSIS THALIANA UBIQUITIN-SPECIFIC PROTEASE 3)Encodes a nuclear ubiquitin-specific protease.O.I.H.G.S.X.
0.3745.00.91At4g12230826831esterase/lipase/thioesterase family proteinF:catalytic activity;P:biological_process unknown;C:cellular_component unknown;BOMPAFVO.I.H.G.S.X.
0.3643.60.91At3g61180825290zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:plasma membrane;PMOFVBO.I.H.G.S.X.
0.3643.60.92At3g54300824597ATVAMP727 (VESICLE-ASSOCIATED MEMBRANE PROTEIN 727)Encodes a member of Synaptobrevin -like protein family. VAMP727 is a R-SNARE and interacts with SYP22/VTI11/SYP51. It is required for trafficking of storage proteins to the protein storage vacuoles (PSV) and also for PSV organization and biogenesis. Loss of function mutations have no phenotype but double mutants with SYP22 are embryo lethal.O.I.H.G.S.X.
0.3643.60.91At4g21450826300vesicle-associated membrane family protein / VAMP family proteinF:structural molecule activity;P:biological_process unknown;C:plasma membrane;MOFPBVO.I.H.G.S.X.
0.3643.60.91At3g54840824649ARA6Encodes a novel Rab-like GTP-ase that is localized to the peripheral membrane of the endosome.O.I.H.G.S.X.
0.3643.60.91At4g25570828662ACYB-2Encodes cytochrome b561.O.I.H.G.S.X.
0.3643.60.93At3g55830824749EPC1 (ECTOPICALLY PARTING CELLS)A member of the Glycosyltransferase Family 64, homologous to Poplar cambium-expressed GT64 gene. The EPC1 protein plays a critical role during plant development in maintaining the integrity of organs via cell-cell adhesion, thereby providing mechanical strength and facilitating the movement of metabolites throughout the plant.O.I.H.G.S.X.
0.3541.60.92At3g51520824315diacylglycerol acyltransferase familyF:diacylglycerol O-acyltransferase activity, transferase activity, transferring acyl groups other than amino-acyl groups;P:biological_process unknown;C:cellular_component unknown;MBFOPO.I.H.G.S.X.
0.3541.60.91At5g21090832233leucine-rich repeat protein, putativeF:protein binding;P:signal transduction;C:endomembrane system;PMOBFAO.I.H.G.S.X.
0.3541.60.91At3g61790825352seven in absentia (SINA) family proteinF:ubiquitin-protein ligase activity, protein binding, zinc ion binding;P:multicellular organismal development, ubiquitin-dependent protein catabolic process, protein ubiquitination;C:nucleus;MPOFO.I.H.G.S.X.
0.3439.80.92At1g32790840173RNA-binding protein, putativeRNA-binding protein, putative, similar to RNA-binding protein GB:CAB40027 GI:4539439 from (Arabidopsis thaliana).Member of a family of PAB2 binding domain proteins.O.I.H.G.S.X.
0.3439.80.92At5g02040831904PRA1.A1 (PRENYLATED RAB ACCEPTOR 1.A1)F:molecular_function unknown;P:vesicle-mediated transport;C:endoplasmic reticulum;MPFO.I.H.G.S.X.
0.3133.80.92At1g71190843459SAG18 (SENESCENCE ASSOCIATED GENE 18)Senescence associated gene (SAG). Expression induced by ozone. Encodes a plant-specific protein of unknown function. Based on a personal communication from David Meinke (08/21/2007), this gene is not allelic to TTN4, even though this has been stated previously in a publication.O.I.H.G.S.X.
0.2830.30.92At5g53530835435VPS26A (VACUOLAR PROTEIN SORTING 26A)Homolog of yeast retromer subunit VPS26. Part of a retromer-like protein complex involved in endosome to lysosome protein transport.O.I.H.G.S.X.
0.2522.60.91At5g51400835214unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFO.I.H.G.S.X.
0.2522.60.91At5g61500836271ATG3F:molecular_function unknown;P:autophagy;C:cellular_component unknown;MFOPO.I.H.G.S.X.

Click More genes

Link to AtGenExpress Visualization Tool



Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
103.699.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
85.299.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
77.899.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
65.799.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.199.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.999.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.899.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.499.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.099.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.899.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.199.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.999.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
40.699.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.499.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.399.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.399.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.199.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
40.099.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.899.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.099.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
37.599.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.899.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.899.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.699.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.799.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.699.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.199.5E-ATMX-35-raw-cel-1574334816
17.999.5GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
17.699.5GSM133969Birnbaum_1-20_LRC-2_Rep2_ATH1GSE5749A gene expression map of the Arabidopsis rootLink to GEO
16.999.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.399.4GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
13.699.4GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
12.299.3E-ATMX-35-raw-cel-1574334832
11.799.3GSM133754Turner_A-8-Turne-WT-Base2_SLDGSE5729Role of COV in vascular patterningLink to GEO
11.799.3GSM184478Lateral Root Cap root cells 2hr KCl control treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.699.3GSM133721Deeken_A-1-Deeke-Tum_SLD_REP2GSE5725Agrobacterium tumefaciens-induced tumour development of Arabidopsis thalianaLink to GEO
11.599.3GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.499.3E-MEXP-265-raw-cel-414618394
11.299.2E-MEXP-807-raw-cel-1173273223
11.099.2GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.899.2E-MEXP-807-raw-cel-1173273060
10.599.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.499.2GSM133753Turner_A-7-Turne-WT-Base1_SLDGSE5729Role of COV in vascular patterningLink to GEO
10.099.2GSM218590Protoplasted root cells 2hr transitory KNO3 treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.199.1GSM142636MC002_ATH1_A5.2-dubos-5kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.099.1GSM142637MC002_ATH1_A5.3-dubos-5kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
8.799.0E-MEXP-807-raw-cel-1173273170

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0652GO:0007033A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole.Link to AmiGO
0.0552GO:0006623The process of directing proteins towards the vacuole, usually using signals contained within the protein.Link to AmiGO
0.0502GO:0009742A series of molecular signals mediated by the detection of brassinosteroid.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.098504130SNARE interactions in vesicular transportLink to KEGG PATHWAY
0.031104140Regulation of autophagyLink to KEGG PATHWAY
0.029104650Natural killer cell mediated cytotoxicityLink to KEGG PATHWAY

Inter-species module comparison

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays



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