Co-expression analysis

Gene ID At3g26690
Gene name ATNUDX13 (ARABIDOPSIS THALIANA NUDIX HYDROLASE HOMOLOG 13)
Module size 23 genes
NF 0.33
%ile 42.1



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
0.5469.51.00At3g26690822281ATNUDX13 (ARABIDOPSIS THALIANA NUDIX HYDROLASE HOMOLOG 13)Encodes AtNUDT13, a mitochondrial Nudix hydrolase specific for long-chain diadenosine polyphosphates.O.I.H.G.S.X.
0.4963.50.70At1g78340844169ATGSTU22 (GLUTATHIONE S-TRANSFERASE TAU 22)Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002).O.I.H.G.S.X.
0.4862.50.71At2g27000817242CYP705A8member of CYP705AO.I.H.G.S.X.
0.4761.20.70At5g39970833994catalyticF:catalytic activity;P:biological_process unknown;C:anchored to membrane;OBPMAFO.I.H.G.S.X.
0.4558.30.67At3g19390821473cysteine proteinase, putative / thiol protease, putativeF:cysteine-type endopeptidase activity, cysteine-type peptidase activity;P:proteolysis;C:endomembrane system;MOPBVAFO.I.H.G.S.X.
0.4253.90.67At1g69810843317WRKY36member of WRKY Transcription Factor; Group II-bO.I.H.G.S.X.
0.4152.40.70At5g17330831599GADEncodes one of two isoforms of glutamate decarboxylase.O.I.H.G.S.X.
0.4152.40.71At2g14100815896CYP705A13a member of the cytochrome P450 familyO.I.H.G.S.X.
0.4050.80.68At5g44380834464FAD-binding domain-containing proteinF:electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity;P:response to oxidative stress;C:cell wall;BFOPAMO.I.H.G.S.X.
0.4050.80.68At5g54020835485zinc ion bindingF:zinc ion binding;P:intracellular signaling cascade;C:intracellular;PMOFO.I.H.G.S.X.
0.3745.00.67At1g773308440691-aminocyclopropane-1-carboxylate oxidase, putative / ACC oxidase, putativesimilar to 1-aminocyclopropane-1-carboxylate oxidase GI:3386565 from (Sorghum bicolor)O.I.H.G.S.X.
0.3643.60.67At2g04680815011DC1 domain-containing proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFO.I.H.G.S.X.
0.3439.80.67At3g20960821646CYP705A33member of CYP705AO.I.H.G.S.X.
0.3338.10.67At3g05890819758RCI2B (RARE-COLD-INDUCIBLE 2B)F:unknown;P:response to cold;C:integral to membrane;BFPMOO.I.H.G.S.X.
0.3338.10.67At3g53480824516PDR9 (PLEIOTROPIC DRUG RESISTANCE 9)F:ATPase activity, coupled to transmembrane movement of substances;P:multidrug transport;C:plasma membrane;BOMAFPVO.I.H.G.S.X.
0.2930.30.67At4g13130826927DC1 domain-containing proteinF:protein binding, zinc ion binding;P:biological_process unknown;C:chloroplast envelope;PMOO.I.H.G.S.X.
0.2624.40.68At2g24610816997ATCNGC14member of Cyclic nucleotide gated channel familyO.I.H.G.S.X.
0.2522.60.70At2g39110818497protein kinase, putativeF:protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MPOBFVAO.I.H.G.S.X.
0.2420.70.69At1g22440838850alcohol dehydrogenase, putativeF:oxidoreductase activity, binding, catalytic activity, zinc ion binding;P:oxidation reduction, metabolic process;C:cellular_component unknown;BOPFMAVO.I.H.G.S.X.
0.2319.30.68At4g13660827000PRR2 (PINORESINOL REDUCTASE 2)Encodes a pinoresinol reductase involved in lignan biosynthesis. Expressed strongly in roots and less strongly in stems. Shows preference for pinoresinol and not lariciresinol.O.I.H.G.S.X.
0.1811.40.67At1g66450842963DC1 domain-containing proteinF:protein binding, zinc ion binding;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.157.80.69At3g24670822063pectate lyase family proteinF:pectate lyase activity;P:biological_process unknown;C:endomembrane system;PBFOO.I.H.G.S.X.
0.092.80.71At2g30500817600kinase interacting family proteinF:unknown;P:unknown;C:unknown;MOBFPAVO.I.H.G.S.X.

VF%ileCCGene IDRepr. IDGene nameFunc.O.I.H.G.S.X.Other DB
0.5065.30.73At1g51420841567SPP1 (SUCROSE-PHOSPHATASE 1)F:phosphatase activity, magnesium ion binding, sucrose-phosphatase activity, catalytic activity;P:sucrose biosynthetic process, metabolic process;C:plasma membrane;BPOO.I.H.G.S.X.
0.4050.80.66At5g51060835179RHD2 (ROOT HAIR DEFECTIVE 2)RHD2 (along with RHD3 and RHD4) is required for normal root hair elongation. Has NADPH oxidase activity. Gene is expressed in the elongation and differention zone in trichoblasts and elongating root hairs. RDH2 is localized to the growing tips of root hair cells. It is required for the production of reactive oxygen species in response to extracellular ATP stimulus. The increase in ROS production stimulates Ca2+ influx.O.I.H.G.S.X.
0.3948.40.63At1g53180841752unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OPMFO.I.H.G.S.X.
0.3846.70.64At5g10720830938AHK5 (ARABIDOPSIS HISTIDINE KINASE 5)member of Histidine KinaseO.I.H.G.S.X.
0.3846.70.66At3g46720823825UDP-glucoronosyl/UDP-glucosyl transferase family proteinF:transferase activity, transferring hexosyl groups, UDP-glycosyltransferase activity, transferase activity, transferring glycosyl groups;P:metabolic process;C:cellular_component unknown;PMBVOFO.I.H.G.S.X.
0.3643.60.62At2g34830818048WRKY35 (WRKY DNA-binding protein 35)member of WRKY Transcription Factor; Group II-eO.I.H.G.S.X.
0.3643.60.61At3g25790822170myb family transcription factorF:transcription factor activity, DNA binding;P:regulation of transcription;C:unknown;POMO.I.H.G.S.X.
0.3643.60.60At5g01040831877LAC8 (laccase 8)putative laccase, knockout mutant showed early floweringO.I.H.G.S.X.
0.3541.60.64At1g15210838087PDR7 (PLEIOTROPIC DRUG RESISTANCE 7)F:ATPase activity, coupled to transmembrane movement of substances;P:multidrug transport;C:plasma membrane, chloroplast, membrane;BOMFAPVO.I.H.G.S.X.
0.3439.80.58At3g48920824053AtMYB45 (myb domain protein 45)Member of the R2R3 factor gene family.O.I.H.G.S.X.
0.3439.80.64At4g30170829140peroxidase, putativeF:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:endomembrane system;PFOBO.I.H.G.S.X.
0.3338.10.64At1g68150843143WRKY9member of WRKY Transcription Factor; Group II-bO.I.H.G.S.X.
0.3338.10.65At3g01220821232ATHB20 (ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 20)Encodes a homeodomain leucine zipper class I (HD-Zip I) protein, its expression is auxin-inducible and dependent on MP gene activity.O.I.H.G.S.X.
0.3338.10.64At5g44110834434POP1Encodes a member of the NAP subfamily of ABC transporters.O.I.H.G.S.X.
0.3235.70.65At1g50520841474CYP705A27member of CYP705AO.I.H.G.S.X.
0.3235.70.57At5g47950834846transferase family proteinF:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFOO.I.H.G.S.X.
0.3235.70.59At1g17060838276CYP72C1 (CYTOCHROME P450 72C1)Encodes a protein with similarity to other cytochrome P450's and is a homolog of BAS1. Over expression causes a dwarf phenotype resembling brassinolide resistant mutants. Double mutant analysis of sob7/bas1 loss of function mutants suggests these genes have redundant functions in light responsiveness. SOB7 may function in metabolizing brassinolides. Expressed in leaf, root, stem and silique but expression highest in flower and cauline leaves. Dominant overexpressing plants have dwarf phenotype, short siliques/seeds, rounded dark green leaves and short hypocotyls in light and dark. Loss of function alleles result in plants with long hypocotyls.O.I.H.G.S.X.
0.3133.80.63At2g45400819146BEN1involved in the regulation of brassinosteroid metabolic pathwayO.I.H.G.S.X.
0.3133.80.58At5g48560834912basic helix-loop-helix (bHLH) family proteinF:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;POMFBVO.I.H.G.S.X.
0.3032.10.59At3g62280825401carboxylesterase/ hydrolase, acting on ester bondsF:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBFOMO.I.H.G.S.X.
0.3032.10.65At3g14940820723ATPPC3 (PHOSPHOENOLPYRUVATE CARBOXYLASE 3)One of four genes encoding phosphoenolpyruvate carboxylase, its mRNA is most abundantly expressed in roots and siliques.O.I.H.G.S.X.
0.3032.10.63At3g50300824192transferase family proteinF:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFOO.I.H.G.S.X.
0.3032.10.59At5g44610834489MAP18 (Microtubule-associated Protein 18)Encodes a protein of unknown function with seven repeated VEEKK motifs. RNAi and overexpression experiments suggest that the gene is not involved in cell division but might be consequential for cell shape of epidermal and cortical cells. The protein encoded by this gene binds to cortical microtubules and inhibits tubulin polymerization.O.I.H.G.S.X.
0.2930.30.62At3g07000819885DC1 domain-containing proteinF:protein binding, zinc ion binding;P:intracellular signaling cascade;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.2930.30.63At2g25810817123TIP4F:water channel activity;P:transport;C:integral to membrane, membrane;BPMOFAO.I.H.G.S.X.
0.2830.30.65At5g06860830577PGIP1 (POLYGALACTURONASE INHIBITING PROTEIN 1)Encodes a polygalacturonase inhibiting protein involved in defense response. PGIPs inhibit the function of cell wall pectin degrading enzymes such as those produced by fungal pathogens. PGIP1 is induced by fungal infection.O.I.H.G.S.X.
0.2830.30.65At4g21600828246ENDO5 (endonuclease 5)Encodes a protein with mismatch-specific endonuclease activity with a preference for T/G, A/G, and G/G of single base mismatches. It also has the ability to cleave indel types of mismatches (heteroduplexes with loops).O.I.H.G.S.X.
0.2830.30.64At5g01490831754CAX4 (CATION EXCHANGER 4)Encodes a cation/proton antiporter, a member of Low affinity calcium antiporter CAX2 family.O.I.H.G.S.X.
0.2830.30.57At1g80240844364unknown proteinF:molecular_function unknown;P:biological_process unknown;C:plant-type cell wall;PBO.I.H.G.S.X.
0.2726.20.64At3g20130821556CYP705A22member of CYP705AO.I.H.G.S.X.
0.2726.20.62At3g01190821314peroxidase 27 (PER27) (P27) (PRXR7)F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:endomembrane system;PFOBMO.I.H.G.S.X.
0.2726.20.57At2g22470816779AGP2 (ARABINOGALACTAN PROTEIN 2)Encodes arabinogalactan-protein (AGP2).O.I.H.G.S.X.
0.2726.20.59At1g17180838289ATGSTU25 (GLUTATHIONE S-TRANSFERASE TAU 25)Encodes glutathione transferase belonging to the tau class of GSTs. Naming convention according to Wagner et al. (2002).O.I.H.G.S.X.
0.2726.20.59At2g41660818764MIZ1 (mizu-kussei 1)Essential for hydrotropism in roots. Mutant roots are defective in hydrotropism, and have slightly reduced phototropism and modified wavy growth response. Has normal gravitropism and root elongation.O.I.H.G.S.X.
0.2624.40.60At2g02610814790DC1 domain-containing proteinF:unknown;P:unknown;C:cellular_component unknown;POMO.I.H.G.S.X.
0.2624.40.64At5g10830830950embryo-abundant protein-relatedF:methyltransferase activity;P:metabolic process;C:cellular_component unknown;BPFMOAO.I.H.G.S.X.
0.2624.40.64At1g18980838479germin-like protein, putativeF:manganese ion binding, nutrient reservoir activity;P:biological_process unknown;C:endomembrane system, apoplast;PBFOO.I.H.G.S.X.
0.2522.60.59At2g15490816041UGT73B4 (UDP-GLYCOSYLTRANSFERASE 73B4)F:quercetin 3-O-glucosyltransferase activity, quercetin 7-O-glucosyltransferase activity, UDP-glycosyltransferase activity, UDP-glucosyltransferase activity, transferase activity, transferring glycosyl groups;P:response to other organism;C:endomembrane system;PMVBOFO.I.H.G.S.X.
0.2522.60.61At5g66690836802UGT72E2UGT72E2 is an UDPG:coniferyl alcohol glucosyltransferase which glucosylates sinapyl- and coniferyl aldehydes as well as sinapyl- and coniferyl alcohol. The enzyme is thought to be involved in lignin metabolism. A knockdown mutant line (72E2KD) was obtained using RNAi silencing. A twofold reduction in coniferyl alcohol 4-O-glucoside and sinapyl alcohol 4-O-glucoside was detected in this line compared to wildtype. In comparison, both knockout and knockdown lines of UGT72E1 and UGT72E3, respectively, failed to display the same reduction in phenylpropanoid 4-O-glucosides.O.I.H.G.S.X.
0.2522.60.59At3g21680821722unknown proteinF:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;PO.I.H.G.S.X.
0.2522.60.59At2g18980816415peroxidase, putativeF:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:endomembrane system;PFOBMO.I.H.G.S.X.

Link to AtGenExpress Visualization Tool



Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
74.799.9GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
71.299.9GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
62.999.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
61.499.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
56.799.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
54.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.999.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.099.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.899.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.599.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.799.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.099.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.599.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.299.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
32.699.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.599.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.299.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.199.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.799.7GSM131699ATGE_81_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
26.099.7GSM131698ATGE_81_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
24.799.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.299.6GSM131697ATGE_81_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
23.899.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
23.199.6GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.499.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
18.999.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.799.5GSM226554Slice12JWGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
16.299.5GSM131695ATGE_79_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
14.799.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.799.4E-ATMX-1-raw-cel-1112746154
14.199.4E-MEXP-1592-raw-cel-1617526848
13.699.4GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
13.499.4E-MEXP-807-raw-cel-1173273196
12.499.3GSM265431Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
12.399.3E-MEXP-807-raw-cel-1173273088
11.799.3GSM131696ATGE_79_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.499.3GSM265430Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 1GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
11.499.3GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.499.3GSM265422Arabidopsis, root, longitudinal zone 3, standard conditions, rep1GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
11.399.3E-MEXP-1592-raw-cel-1617526912
10.999.2GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.799.2GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.599.2E-MEXP-1592-raw-cel-1617526944
10.499.2GSM290756root - 01% oxygen - 30min - DGSE11558transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plantsLink to GEO
10.499.2GSM131694ATGE_79_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
10.199.2E-ATMX-1-raw-cel-1112746267
9.699.1GSM290755root - 01% oxygen - 2h - FGSE11558transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plantsLink to GEO
9.599.1E-MEXP-807-raw-cel-1173273060
9.399.1E-MEXP-1592-raw-cel-1617526880
9.399.1GSM184922Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.199.1GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.099.1GSM131237AtGen_6-0221_Control-Roots-1.0h_Rep1GSE5620AtGenExpress: Stress Treatments (Control plants)Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0561GO:0006811The directed movement of charged atoms or small charged molecules into, out of, within or between cells.Link to AmiGO
0.0511GO:0009807The chemical reactions and pathways resulting in the formation of lignans, any member of a class of plant metabolites related to lignins. Lignans are usually found as phenylpropanoid dimers in which the phenylpropanoid units are linked tail to tail and thus having a 2,3 dibenzylbutane skeleton, but higher oligomers can also exist.Link to AmiGO
0.0321GO:0006813The directed movement of potassium ions (K+) into, out of, within or between cells.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.074100430Taurine and hypotaurine metabolismLink to KEGG PATHWAY
0.050100410beta-Alanine metabolismLink to KEGG PATHWAY
0.048100640Propanoate metabolismLink 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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