Co-expression analysis

Gene ID At3g56350
Gene name superoxide dismutase (Mn), putative / manganese superoxide dismutase, putative
Module size 30 genes
NF 0.72
%ile 90.1



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
1.00100.01.00At3g56350824802superoxide dismutase (Mn), putative / manganese superoxide dismutase, putativeF:superoxide dismutase activity, metal ion binding;P:superoxide metabolic process, removal of superoxide radicals;C:mitochondrion, endomembrane system;BOFMPAVO.I.H.G.S.X.
0.8592.40.90At5g57550835859XTR3 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 3)xyloglucan endotransglycosylase-related protein (XTR3)O.I.H.G.S.X.
0.8592.40.96At4g10020826593AtHSD5 (hydroxysteroid dehydrogenase 5)F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:endomembrane system;BOMFPAVO.I.H.G.S.X.
0.8290.90.94At2g33520817917-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFO.I.H.G.S.X.
0.8190.40.97At5g45690834608unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BPFO.I.H.G.S.X.
0.8190.40.94At5g22470832308NAD+ ADP-ribosyltransferaseF:NAD+ ADP-ribosyltransferase activity;P:protein amino acid ADP-ribosylation;C:intracellular, nucleus;MOPFBVO.I.H.G.S.X.
0.7989.10.92At5g01670831701aldose reductase, putativeF:oxidoreductase activity;P:oxidation reduction;C:unknown;BMOFPAO.I.H.G.S.X.
0.7888.60.93At3g05260819690short-chain dehydrogenase/reductase (SDR) family proteinF:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.7888.60.93At4g09600826545GASA3 (GAST1 PROTEIN HOMOLOG 3)One of GASA gene family which is related to a GA-stimulated transcript (GAST) from tomato.O.I.H.G.S.X.
0.7788.00.92At3g50980824262XERO1 (DEHYDRIN XERO 1)F:molecular_function unknown;P:response to water, response to stress;C:cellular_component unknown;PMO.I.H.G.S.X.
0.7788.00.96At1g05510837053-Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.O.I.H.G.S.X.
0.7687.40.92At4g09610826546GASA2 (GAST1 PROTEIN HOMOLOG 2)F:molecular_function unknown;P:response to gibberellin stimulus;C:endomembrane system;PO.I.H.G.S.X.
0.7687.40.91At3g12960820482unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7687.40.95At5g55240835617caleosin-related family protein / embryo-specific protein, putativeF:calcium ion binding;P:biological_process unknown;C:cellular_component unknown;PFOO.I.H.G.S.X.
0.7586.90.91At3g11050820276ATFER2 (ferritin 2)F:oxidoreductase activity, ferric iron binding, binding, transition metal ion binding;P:response to oxidative stress, cellular iron ion homeostasis, response to abscisic acid stimulus, iron ion transport;C:chloroplast;MBPOAFO.I.H.G.S.X.
0.7385.50.91At1g27990839692unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7385.50.89At4g31830829312unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7284.80.90At2g19900816509ATNADP-ME1 (NADP-malic enzyme 1)The malic enzyme (EC 1.1.1.40) encoded by AtNADP-ME1 is expressed in response to developmental and cell-specific signals.O.I.H.G.S.X.
0.7284.80.91At3g51810824344EM1 (LATE EMBRYOGENESIS ABUNDANT 1)Encodes a ABA-inducible protein that accumulates during seed maturation, in parallel with its corresponding mRNA but with a 3 d delay. During germination, AtEm1 protein undergoes two successive cleavages before being degraded. Both proteins are more stable than the corresponding mRNA. The gene can be activated by the basic leucine zipper transcription factor ABI5. Expressed predominantly in provascular tissues with the strongest expression in the root tip.O.I.H.G.S.X.
0.7083.50.92At5g55750835669hydroxyproline-rich glycoprotein family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBVAO.I.H.G.S.X.
0.6781.60.90At1g02700839492unknown proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion;PMFOO.I.H.G.S.X.
0.6781.60.92At1g54870841926binding / catalytic/ oxidoreductaseF:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:chloroplast;BOMFPAVO.I.H.G.S.X.
0.6781.60.89At2g21490816688LEA (DEHYDRIN LEA)F:molecular_function unknown;P:response to water, response to stress;C:cellular_component unknown;PMFOBVO.I.H.G.S.X.
0.6680.10.91At1g29680839845unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BPFO.I.H.G.S.X.
0.6579.60.90At3g58450825014universal stress protein (USP) family proteinF:molecular_function unknown;P:response to stress;C:cellular_component unknown;BPAOFMO.I.H.G.S.X.
0.6277.30.90At2g23640816896reticulon family protein (RTNLB13)F:molecular_function unknown;P:biological_process unknown;C:endoplasmic reticulum;MPOO.I.H.G.S.X.
0.6176.70.91At1g14950838060major latex protein-related / MLP-relatedF:molecular_function unknown;P:response to biotic stimulus, defense response;C:cellular_component unknown;PO.I.H.G.S.X.
0.6075.70.91At1g17810838359BETA-TIP (BETA-TONOPLAST INTRINSIC PROTEIN)beta-tonoplast intrinsic protein (beta-TIP) mRNA, completeO.I.H.G.S.X.
0.5673.00.90At1g73190843653TIP3Moves to the Protein Storage Vacuole in a Golgi independent mannerO.I.H.G.S.X.
0.5673.00.90At5g50600835129AtHSD1 (hydroxysteroid dehydrogenase 1)F:oxidoreductase activity, binding, catalytic activity;P:response to brassinosteroid stimulus, response to abscisic acid stimulus;C:endomembrane system;BOMFPAVO.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
80.499.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
71.699.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
55.999.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
51.499.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.099.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.599.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.499.8GSM142734DH001_ATH1_A1-UNM1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
43.499.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.999.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.499.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.799.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.699.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
41.599.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.699.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
38.699.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.499.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
38.399.8GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
37.599.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.399.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
35.199.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.199.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.399.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.399.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.299.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.799.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.899.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.999.7GSM142737DH001_ATH1_A4-UNM2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
20.999.6E-MEXP-1443-raw-cel-1581869573
20.099.6GSM142738DH001_ATH1_A5-BCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
16.999.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.499.4GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.599.4GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
13.099.4E-MEXP-1443-raw-cel-1581869515
12.199.3GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.499.3GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
11.199.2GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.999.2GSM269813WT leaf-drought-rep1GSE10670Global expression profiling of wild type and transgenic Arabidopsis plants in response to water stressLink to GEO
10.599.2E-ATMX-33-raw-cel-1562596241

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1002GO:0009415A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water stimulus.Link to AmiGO
0.0651GO:0006801The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.Link to AmiGO
0.0611GO:0006471The transfer, from NAD, of ADP-ribose to protein amino acids.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.021100620Pyruvate metabolismLink to KEGG PATHWAY
0.019100710Carbon fixation in photosynthetic organismsLink to KEGG PATHWAY
0.011101066Biosynthesis of alkaloids derived from terpenoid and polyketideLink 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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