Co-expression analysis

Gene ID At2g19900
Gene name ATNADP-ME1 (NADP-malic enzyme 1)
Module size 33 genes
NF 0.77
%ile 93.3



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
1.00100.01.00At2g19900816509ATNADP-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.
0.9597.00.95At5g01670831701aldose reductase, putativeF:oxidoreductase activity;P:oxidation reduction;C:unknown;BMOFPAO.I.H.G.S.X.
0.8793.50.94At1g27990839692unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8592.40.91At5g55750835669hydroxyproline-rich glycoprotein family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBVAO.I.H.G.S.X.
0.8491.90.88At4g09610826546GASA2 (GAST1 PROTEIN HOMOLOG 2)F:molecular_function unknown;P:response to gibberellin stimulus;C:endomembrane system;PO.I.H.G.S.X.
0.8391.40.93At4g09600826545GASA3 (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.
0.8391.40.91At1g75490843885DNA binding / transcription factorencodes a member of the DREB subfamily A-2 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are eight members in this subfamily including DREB2A AND DREB2B that are involved in response to drought.O.I.H.G.S.X.
0.8391.40.91At3g05260819690short-chain dehydrogenase/reductase (SDR) family proteinF:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.8290.90.94At1g02700839492unknown proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion;PMFOO.I.H.G.S.X.
0.8290.90.88At2g19320816449unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8290.90.92At3g11050820276ATFER2 (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.
0.8190.40.92At4g10020826593AtHSD5 (hydroxysteroid dehydrogenase 5)F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:endomembrane system;BOMFPAVO.I.H.G.S.X.
0.8190.40.93At5g22470832308NAD+ ADP-ribosyltransferaseF:NAD+ ADP-ribosyltransferase activity;P:protein amino acid ADP-ribosylation;C:intracellular, nucleus;MOPFBVO.I.H.G.S.X.
0.8089.80.91At2g33520817917-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFO.I.H.G.S.X.
0.8089.80.88At3g12960820482unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7989.10.90At5g66110836743metal ion bindingF:metal ion binding;P:metal ion transport;C:plasma membrane;PFMO.I.H.G.S.X.
0.7888.60.92At3g50980824262XERO1 (DEHYDRIN XERO 1)F:molecular_function unknown;P:response to water, response to stress;C:cellular_component unknown;PMO.I.H.G.S.X.
0.7888.60.91At3g58450825014universal stress protein (USP) family proteinF:molecular_function unknown;P:response to stress;C:cellular_component unknown;BPAOFMO.I.H.G.S.X.
0.7788.00.90At5g45310834567unknown proteinF:unknown;P:unknown;C:endomembrane system;OMVBFPAO.I.H.G.S.X.
0.7687.40.90At4g21020827849late embryogenesis abundant domain-containing protein / LEA domain-containing proteinF:unknown;P:embryonic development ending in seed dormancy;C:unknown;OMBPFVAO.I.H.G.S.X.
0.7687.40.90At4g27530828862unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7687.40.92At5g42290834234transcription activator-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.7586.90.90At2g23640816896reticulon family protein (RTNLB13)F:molecular_function unknown;P:biological_process unknown;C:endoplasmic reticulum;MPOO.I.H.G.S.X.
0.7385.50.90At3g56350824802superoxide 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.
0.7184.20.89At3g51810824344EM1 (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.
0.7083.50.91At5g55240835617caleosin-related family protein / embryo-specific protein, putativeF:calcium ion binding;P:biological_process unknown;C:cellular_component unknown;PFOO.I.H.G.S.X.
0.7083.50.90At5g43770834399proline-rich family proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;MBPOFVAO.I.H.G.S.X.
0.7083.50.90At5g01300830983phosphatidylethanolamine-binding family proteinF:phosphatidylethanolamine binding;P:biological_process unknown;C:cellular_component unknown;BOAPFO.I.H.G.S.X.
0.6982.90.91At1g29680839845unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BPFO.I.H.G.S.X.
0.6882.20.91At3g17520821017late embryogenesis abundant domain-containing protein / LEA domain-containing proteinF:unknown;P:embryonic development ending in seed dormancy;C:endomembrane system;MOBFPVAO.I.H.G.S.X.
0.6680.10.89At5g45690834608unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BPFO.I.H.G.S.X.
0.6378.10.90At4g31830829312unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6075.70.88At1g05510837053-Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.O.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
154.399.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
58.099.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
49.499.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
48.399.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.099.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.499.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.599.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.599.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.299.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.599.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.599.8GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
39.499.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.399.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.199.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.299.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.199.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.099.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.399.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
35.299.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.099.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.799.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.599.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.799.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.199.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.099.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.899.6GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
19.199.6E-MEXP-1344-raw-cel-1559561563
19.099.5E-MEXP-1443-raw-cel-1581869573
17.299.5E-MEXP-1345-raw-cel-1559561139
16.299.5E-MEXP-1345-raw-cel-1559561169
14.499.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.199.4E-MEXP-1345-raw-cel-1559561229
13.599.4GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.399.4E-MEXP-1344-raw-cel-1559561593
13.199.4E-MEXP-1345-raw-cel-1559561259
13.099.4E-MEXP-1345-raw-cel-1559561289
12.799.3E-MEXP-1344-raw-cel-1559561683
12.799.3E-MEXP-1345-raw-cel-1559561199
11.999.3E-MEXP-1443-raw-cel-1581869515
11.999.3GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.699.2E-MEXP-1344-raw-cel-1559561713
10.099.2GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.499.1E-MEXP-1344-raw-cel-1559561623
9.399.1GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.999.0E-ATMX-33-raw-cel-1562596241

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0591GO:0006801The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.Link to AmiGO
0.0561GO:0006471The transfer, from NAD, of ADP-ribose to protein amino acids.Link to AmiGO
0.0491GO:0019430Any process involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.020100620Pyruvate 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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