Co-expression analysis

Gene ID At2g42560
Gene name late embryogenesis abundant domain-containing protein / LEA domain-containing protein
Module size 50 genes
NF 0.78
%ile 93.4



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
1.00100.01.00At2g42560818856late embryogenesis abundant domain-containing protein / LEA domain-containing proteinF:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;BOMPFVAO.I.H.G.S.X.
0.9697.30.91At5g55750835669hydroxyproline-rich glycoprotein family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBVAO.I.H.G.S.X.
0.9195.60.89At1g75490843885DNA 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.
0.8994.60.82At1g26400839182FAD-binding domain-containing proteinF:electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity;P:unknown;C:endomembrane system;FBPOAMO.I.H.G.S.X.
0.8994.60.80At5g607608361972-phosphoglycerate kinase-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPBAFVO.I.H.G.S.X.
0.8994.60.89At1g27990839692unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8994.60.89At2g19320816449unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8994.60.89At3g05260819690short-chain dehydrogenase/reductase (SDR) family proteinF:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:cellular_component unknown;BOMFPAVO.I.H.G.S.X.
0.8894.00.88At1g02700839492unknown proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion;PMFOO.I.H.G.S.X.
0.8894.00.91At4g27530828862unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8793.50.91At4g21020827849late 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.
0.8793.50.85At2g19900816509ATNADP-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.
0.8793.50.87At5g01670831701aldose reductase, putativeF:oxidoreductase activity;P:oxidation reduction;C:unknown;BMOFPAO.I.H.G.S.X.
0.8592.40.88At3g22500821821ATECP31late embryogenesis abundant (LEA) proteinO.I.H.G.S.X.
0.8592.40.89At3g61040825276CYP76C7encodes a protein with cytochrome P450 domainO.I.H.G.S.X.
0.8592.40.83At2g23640816896reticulon family protein (RTNLB13)F:molecular_function unknown;P:biological_process unknown;C:endoplasmic reticulum;MPOO.I.H.G.S.X.
0.8491.90.81At5g45310834567unknown proteinF:unknown;P:unknown;C:endomembrane system;OMVBFPAO.I.H.G.S.X.
0.8391.40.85At5g42290834234transcription activator-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.8391.40.87At4g18650827599transcription factor-relatedF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PMO.I.H.G.S.X.
0.8290.90.84At3g58450825014universal stress protein (USP) family proteinF:molecular_function unknown;P:response to stress;C:cellular_component unknown;BPAOFMO.I.H.G.S.X.
0.8290.90.81At5g43770834399proline-rich family proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;MBPOFVAO.I.H.G.S.X.
0.8290.90.80At5g66110836743metal ion bindingF:metal ion binding;P:metal ion transport;C:plasma membrane;PFMO.I.H.G.S.X.
0.8190.40.81At4g09610826546GASA2 (GAST1 PROTEIN HOMOLOG 2)F:molecular_function unknown;P:response to gibberellin stimulus;C:endomembrane system;PO.I.H.G.S.X.
0.8190.40.83At5g22470832308NAD+ ADP-ribosyltransferaseF:NAD+ ADP-ribosyltransferase activity;P:protein amino acid ADP-ribosylation;C:intracellular, nucleus;MOPFBVO.I.H.G.S.X.
0.8089.80.85At3g11050820276ATFER2 (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.
0.7989.10.82At3g12960820482unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7989.10.83At4g10020826593AtHSD5 (hydroxysteroid dehydrogenase 5)F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:endomembrane system;BOMFPAVO.I.H.G.S.X.
0.7687.40.80At2g23110816843-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.7687.40.81At4g09600826545GASA3 (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.
0.7586.90.76At5g55240835617caleosin-related family protein / embryo-specific protein, putativeF:calcium ion binding;P:biological_process unknown;C:cellular_component unknown;PFOO.I.H.G.S.X.
0.7486.10.76At2g42000818800plant EC metallothionein-like family 15 proteinF:zinc ion binding;P:biological_process unknown;C:unknown;PMOBFO.I.H.G.S.X.
0.7385.50.81At3g50980824262XERO1 (DEHYDRIN XERO 1)F:molecular_function unknown;P:response to water, response to stress;C:cellular_component unknown;PMO.I.H.G.S.X.
0.7284.80.78At1g29680839845unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BPFO.I.H.G.S.X.
0.7284.80.75At5g57550835859XTR3 (XYLOGLUCAN ENDOTRANSGLYCOSYLASE 3)xyloglucan endotransglycosylase-related protein (XTR3)O.I.H.G.S.X.
0.7284.80.75At3g51810824344EM1 (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.
0.7184.20.82At2g33520817917-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFO.I.H.G.S.X.
0.7083.50.78At3g56350824802superoxide 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.
0.7083.50.81At3g17520821017late 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.
0.7083.50.79At2g28420817390lactoylglutathione lyase family protein / glyoxalase I family proteinF:lactoylglutathione lyase activity;P:carbohydrate metabolic process;C:cellular_component unknown;BOPMFAO.I.H.G.S.X.
0.7083.50.83At5g54000835483oxidoreductase, 2OG-Fe(II) oxygenase family proteinF:oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, oxidoreductase activity;P:biological_process unknown;C:cellular_component unknown;POBFMO.I.H.G.S.X.
0.6982.90.83At5g45830834623DOG1 (DELAY OF GERMINATION 1)Encodes DOG1 (DELAY OF GERMINATION 1). A quantitative trait locus involved in the control of seed dormancy. Belongs to a novel plant-specific gene family whose members include: DOG1-like 1-4 (DOGL1-4, At4g18660, At4g18680, At4g18690, At4g18650 respectively) and DOG1. DOG1 expression is seed-specific.O.I.H.G.S.X.
0.6882.20.77At5g01300830983phosphatidylethanolamine-binding family proteinF:phosphatidylethanolamine binding;P:biological_process unknown;C:cellular_component unknown;BOAPFO.I.H.G.S.X.
0.6882.20.77At5g16460831507-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.6579.60.78At5g45690834608unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BPFO.I.H.G.S.X.
0.6579.60.74At1g72100843541late embryogenesis abundant domain-containing protein / LEA domain-containing proteinF:unknown;P:embryonic development ending in seed dormancy;C:endomembrane system;BPOMFAVO.I.H.G.S.X.
0.6478.90.80At3g18570821388glycine-rich protein / oleosinF:molecular_function unknown;P:lipid storage;C:monolayer-surrounded lipid storage body, integral to membrane, membrane;PO.I.H.G.S.X.
0.6478.90.76At1g54870841926binding / catalytic/ oxidoreductaseF:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:chloroplast;BOMFPAVO.I.H.G.S.X.
0.6378.10.80At4g31830829312unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6176.70.78At1g05510837053-Protein is tyrosine-phosphorylated and its phosphorylation state is modulated in response to ABA in Arabidopsis thaliana seeds.O.I.H.G.S.X.
0.6075.70.79At1g17810838359BETA-TIP (BETA-TONOPLAST INTRINSIC PROTEIN)beta-tonoplast intrinsic protein (beta-TIP) mRNA, completeO.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
111.699.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
98.499.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
59.899.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
52.699.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
51.899.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
51.399.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.699.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
48.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
48.199.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.799.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.699.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.699.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.099.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.299.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.899.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.599.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.499.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
43.899.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.399.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.899.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.799.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.399.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.699.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
23.699.6GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
21.399.6GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
21.299.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.799.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.399.6GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
18.899.5GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
12.899.3E-MEXP-1443-raw-cel-1581869573
12.799.3E-MEXP-1344-raw-cel-1559561563
11.599.3E-MEXP-1345-raw-cel-1559561139
10.899.2GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.899.2E-MEXP-1345-raw-cel-1559561169
9.499.1E-MEXP-1345-raw-cel-1559561229
9.099.1GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.099.1E-MEXP-1344-raw-cel-1559561593
8.799.0E-MEXP-1345-raw-cel-1559561259
8.799.0E-MEXP-1345-raw-cel-1559561289

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0391GO:0006801The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.Link to AmiGO
0.0381GO:0006471The transfer, from NAD, of ADP-ribose to protein amino acids.Link to AmiGO
0.0341GO: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
0.017100620Pyruvate metabolismLink to KEGG PATHWAY
0.016100710Carbon fixation in photosynthetic organismsLink to KEGG PATHWAY
0.010101066Biosynthesis 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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