Co-expression analysis

Gene ID At5g45940
Gene name atnudt11 (Arabidopsis thaliana Nudix hydrolase homolog 11)
Module size 72 genes
NF 0.14
%ile 10.2

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
1.00100.01.00At5g45940834634atnudt11 (Arabidopsis thaliana Nudix hydrolase homolog 11)Encodes a CoA pyrophosphatase, also has minor activity of NADH pyrophosphatase. Most strongly expressed in embryo cotyledon and hypocotyl, flower, and phloem of vascular tissue. Over-expression mutant had a bigger plant with wider rosette.O.I.H.G.S.X.
0.2726.20.82At3g57790824949glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family proteinF:polygalacturonase activity;P:carbohydrate metabolic process;C:plasma membrane;PBFOMAVO.I.H.G.S.X.
0.2624.40.81At3g23690821950basic helix-loop-helix (bHLH) family proteinF:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PFMOBO.I.H.G.S.X.
0.2522.60.84At1g03520839471glycosyltransferase family 14 protein / core-2/I-branching enzyme family proteinF:transferase activity, transferring glycosyl groups, acetylglucosaminyltransferase activity;P:carbohydrate biosynthetic process;C:membrane;MPBVOO.I.H.G.S.X.
0.2522.60.83At5g01970830706unknown proteinF:unknown;P:unknown;C:unknown;PMOFBO.I.H.G.S.X.
0.2319.30.81At4g14750827130IQD19 (IQ-domain 19)F:calmodulin binding;P:unknown;C:unknown;PMOFBVAO.I.H.G.S.X.
0.2319.30.82At4g10360826628-F:molecular_function unknown;P:biological_process unknown;C:integral to membrane;MFPOVO.I.H.G.S.X.
0.2115.80.82At4g17530827468ATRAB1CF:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:plasma membrane, vacuole, membrane;MOFPBVAO.I.H.G.S.X.
0.2014.40.81At1g67730843098YBR159Encodes one of the two Arabidopsis homologues to YBR159w encoding a S. cerevisiae beta-ketoacyl reductase (KCR), which catalyzes the first reduction during VLCFA (very long chain fatty acids, >18 carbon) elongation: KCR1 (At1g67730), KCR2 (At1g24470). Complementation of the yeast ybr159Delta mutant demonstrated that the two KCR proteins are divergent and that only AtKCR1 can restore heterologous elongase activity similar to the native yeast KCR gene.O.I.H.G.S.X.
0.2014.40.84At3g50530824217CRK (CDPK-related kinase)CDPK-related kinaseO.I.H.G.S.X.
0.1912.70.84At1g01630839231SEC14 cytosolic factor, putative / phosphoglyceride transfer protein, putativeF:transporter activity;P:transport;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.1811.40.81At4g30550829178glutamine amidotransferase class-I domain-containing proteinF:catalytic activity;P:biological_process unknown;C:endomembrane system;OBAFPMO.I.H.G.S.X.
0.1811.40.81At5g39730833969avirulence-responsive protein-related / avirulence induced gene (AIG) protein-relatedF:molecular_function unknown;P:response to salt stress;C:plasma membrane;POBFAO.I.H.G.S.X.
0.1811.40.81At3g54290824596-F:molecular_function unknown;P:N-terminal protein myristoylation;C:chloroplast;PBOO.I.H.G.S.X.
0.1811.40.82At4g29260829047acid phosphatase class B family proteinF:acid phosphatase activity;P:biological_process unknown;C:plasma membrane, vacuole;PBOMO.I.H.G.S.X.
0.1710.20.81At4g27040828812VPS22F:molecular_function unknown;P:vesicle-mediated transport;C:ESCRT II complex;MFOPO.I.H.G.S.X.
0.1710.20.82At2g41760818775unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBO.I.H.G.S.X.
0.1710.20.81At2g44770819086phagocytosis and cell motility protein ELMO1-relatedF:molecular_function unknown;P:phagocytosis;C:cytoskeleton;MPOFO.I.H.G.S.X.
0.1710.20.82At5g50000835064protein kinase, putativeF:protein serine/threonine/tyrosine kinase activity, kinase activity;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVAO.I.H.G.S.X. proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOO.I.H.G.S.X. bindingF:phosphoinositide binding;P:signal transduction;C:plasma membrane;POMFVO.I.H.G.S.X. (actin-related protein C3)F:structural molecule activity;P:actin filament organization;C:Arp2/3 protein complex;MFOPO.I.H.G.S.X. 4b (APG4b)F:peptidase activity;P:autophagy;C:chloroplast;MOFPO.I.H.G.S.X. (PASTICCINO 2)Protein tyrosine phosphatase-like involved in cell division and differentiation. Interacts with CDKA;1 only in its phosphorylated form, preventing dephosphorylation. Overexpression slowed down cell division in suspension cell cultures at the G2-to-M transition and early mitosis and inhibited Arabidopsis seedling growth. Localized in the cytoplasm of dividing cells but moved into the nucleus upon cell differentiation. Based on complementation of yeast mutant PAS2 has acyl-CoA dehydratase activity. It interacts with CER10, a component of the microsomal fatty acid elongase complex, suggesting a role in synthesis of VLCFAs (very long chain fatty acids).O.I.H.G.S.X. (Casein Kinase I-like 8)F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOPBFVAO.I.H.G.S.X. unknown;P:biological_process unknown;C:integral to membrane;MFPOO.I.H.G.S.X. unknown;P:unknown;C:plasma membrane, vacuole, membrane;POO.I.H.G.S.X. protein, putativeF:molecular_function unknown;P:biological_process unknown;C:membrane;MPBOO.I.H.G.S.X. protein sorting protein, putativeHomologous to yeast VPS33. Forms a complex with VCL1 and AtVPS11. Involved in vacuolar biogenesis.O.I.H.G.S.X. (SYNTAXIN OF PLANTS 132)member of SYP13 Gene FamilyO.I.H.G.S.X. (VACUOLAR PROTEIN SORTING 46.1)F:unknown;P:vesicle-mediated transport;C:cellular_component unknown;MPFOAO.I.H.G.S.X. protein kinase activity;P:regulation of cell cycle;C:cellular_component unknown;FMOPBO.I.H.G.S.X. (PA) domain-containing proteinF:peptidase activity, aspartic-type endopeptidase activity;P:proteolysis;C:plasma membrane;MPOBFO.I.H.G.S.X. (PURPLE ACID PHOSPHATASE 26)F:protein serine/threonine phosphatase activity, acid phosphatase activity;P:biological_process unknown;C:vacuole, plant-type cell wall;PBMOFAO.I.H.G.S.X. (ligand-effect modulator 3) family protein / CDC50 family proteinF:molecular_function unknown;P:biological_process unknown;C:membrane;MOFPO.I.H.G.S.X. (Arabidopsis thaliana glycosyl hydrolase 9B7)F:hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:plasma membrane;PBMOFO.I.H.G.S.X. (phytochrome a signal transduction 1)Member of GRAS gene family. Semi-dominant mutant has a reduced response to far-red light and appears to act early in the phytochrome A signaling pathway.O.I.H.G.S.X. of the two genes encoding subunit B of the trimeric enzyme ATP Citrate lyaseO.I.H.G.S.X. protein sorting 55 family protein / VPS55 family proteinF:transporter activity;P:transport;C:vacuole;MFPOO.I.H.G.S.X. (Abi-1-like 1)Encodes a subunit of the WAVE complex. The WAVE complex is required for activation of ARP2/3 complex which functions in actin microfilament nucleation and branching.O.I.H.G.S.X. unknown;P:autophagy;C:cellular_component unknown;MFOPO.I.H.G.S.X. (VILLIN 2)Encodes a protein with high homology to animal villin.O.I.H.G.S.X. (membrane steroid binding protein 1)Encodes a protein with similarity to progesterone-binding proteins in animals. Has been shown to bind steroids in vitro. Expressed in aerial portions of the plant excluding mature flowers and siliques. Antisense experiments suggest a role in inhibition of hypocotyl cell elongation. Expression is suppressed light grown seedlings transferred to the dark.O.I.H.G.S.X. serum glycoprotein family proteinF:lipid binding;P:biological_process unknown;C:plasma membrane, vacuole;MPOO.I.H.G.S.X. cysteine protease family proteinF:cysteine-type peptidase activity;P:biological_process unknown;C:unknown;MFOPO.I.H.G.S.X. proteinF:unknown;P:biological_process unknown;C:unknown;PMFOO.I.H.G.S.X. a member of copper transporter family and functionally complements a high affinity copper transporter mutant in yeastO.I.H.G.S.X. proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFO.I.H.G.S.X. Dim1 homolog.O.I.H.G.S.X. (CATIONIC AMINO ACID TRANSPORTER 8)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.O.I.H.G.S.X. a ECA1 gametogenesis related family proteinO.I.H.G.S.X. bindingF:clathrin binding;P:unknown;C:unknown;MOFPBO.I.H.G.S.X. of the three genes encoding subunit A of the trimeric protein ATP Citrate Lyase. Antisense ACLA-1 plants cause a reduction in cytosolic acetyl-CoA metabolism and have upregulation of stress-related genes and down-regulation of primary metabolism and growth genes, suggesting the mutation restricts normal growth and developmental processes and puts the plant into a state of stress.O.I.H.G.S.X. proteinF:unknown;P:unknown;C:endomembrane system;PO.I.H.G.S.X. unknown;P:biological_process unknown;C:cellular_component unknown;BAMOFPO.I.H.G.S.X. binding / zinc ion bindingF:protein binding, zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MFOPO.I.H.G.S.X. (CYTOCHROME B5 ISOFORM D)Encodes a cytochrome b5 isoform that localizes to the ER. The C-terminal portion of the protein appears to be capable of inserting into a plant microsomal membrane in vitro and the protein appears to be subject to glycosylation.O.I.H.G.S.X. (VACUOLAR PROTON ATPASE A2)Vacuolar proton ATPase subunit VHA-a isoform 2. Localized in the tonoplast.O.I.H.G.S.X. unknown;P:biological_process unknown;C:plasma membrane;MPFOO.I.H.G.S.X. (ARF-GAP domain 4)A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes. AGD4 belongs to the Class 1, together with AGD1, AGD2, and AGD3.O.I.H.G.S.X. proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOFBO.I.H.G.S.X. (glycolipid transfer protein 1)F:glycolipid transporter activity, glycolipid binding;P:glycolipid transport;C:plasma membrane;MFPOO.I.H.G.S.X. protein-relatedF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BOMFPO.I.H.G.S.X. bindingF:protein binding;P:signal transduction;C:Golgi apparatus;PMBOFAO.I.H.G.S.X. (squamosa promoter-binding protein-like 12)F:transcription factor activity;P:regulation of transcription;C:nucleus;PMOO.I.H.G.S.X. repeat family proteinF:protein binding;P:signal transduction;C:unknown;MPBOFAVO.I.H.G.S.X. unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBVAO.I.H.G.S.X. protein kinaseF:AMP-activated protein kinase activity;P:N-terminal protein myristoylation;C:chloroplast;MFPOBO.I.H.G.S.X. proteinF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;POMBFO.I.H.G.S.X. (CYCLOPHILIN 5)encodes a cyclophilin protein that exhibits peptidylprolyl cis/trans-isomerase and protein refolding activities that were sensitive to cyclosporin A. The protein interacts with GNOM in vitro and is localized to both the cytosolic and membrane fractions. The gene is expressed in the developing embryo.O.I.H.G.S.X. proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X. family proteinF:protein binding, binding;P:intracellular protein transport, vesicle-mediated transport;C:membrane coat, endomembrane system;BMFOPO.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
70.799.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
59.999.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
59.399.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
58.399.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
55.599.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
55.599.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
54.499.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
52.999.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.699.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.299.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.099.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.099.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.399.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.999.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.799.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.499.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.999.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
44.499.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.899.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.599.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.699.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
40.999.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.799.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.599.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
34.899.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
33.999.7GSM133758Lindsey_1-11_heart-stage-root_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
27.499.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.699.4GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
14.199.4GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.299.2GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
9.899.1GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.699.1GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0512GO:0006085The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.Link to AmiGO
0.0432GO:0006914The process by which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.Link to AmiGO
0.0342GO:0009790The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.030200020Citrate cycle (TCA cycle)Link to KEGG PATHWAY
0.029204144EndocytosisLink to KEGG PATHWAY
0.024104140Regulation of autophagyLink to KEGG PATHWAY

Inter-species module comparison

Select a plant to compare co-expressed genes between species.

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