Co-expression analysis

Gene ID At5g25940
Gene name early nodulin-related
Module size 56 genes
NF 0.29
%ile 35.5



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
1.00100.01.00At5g25940832663early nodulin-relatedF:molecular_function unknown;P:unknown;C:mitochondrion;PO.I.H.G.S.X.
0.5570.60.90At3g47810823935MAG1 (MAIGO 1)Homolog of yeast retromer subunit VPS29. Part of a retromer-like protein complex involved in endosome to lysosome protein transport.O.I.H.G.S.X.
0.5267.40.88At5g20090832131unknown proteinF:unknown;P:biological_process unknown;C:mitochondrion, plasma membrane, membrane;MFPOO.I.H.G.S.X.
0.5065.30.88At1g63460842652glutathione peroxidase, putativeF:glutathione peroxidase activity;P:response to oxidative stress;C:cellular_component unknown;OBMPFVO.I.H.G.S.X.
0.4558.30.88At4g02620828221vacuolar ATPase subunit F family proteinF:hydrogen ion transporting ATP synthase activity, rotational mechanism, proton-transporting ATPase activity, rotational mechanism;P:ATP synthesis coupled proton transport;C:plasma membrane, vacuole;MFOPAO.I.H.G.S.X.
0.4355.30.88At2g02510814780unknown proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion, respiratory chain complex I;PFO.I.H.G.S.X.
0.4253.90.88At1g08480837369unknown proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion, plasma membrane, plastid, vacuole;PO.I.H.G.S.X.
0.4152.40.88At1g26550839195peptidyl-prolyl cis-trans isomerase PPIC-type family proteinF:isomerase activity;P:biological_process unknown;C:cellular_component unknown;BOMFPAO.I.H.G.S.X.
0.4152.40.89At4g37830829939cytochrome c oxidase-relatedF:cytochrome-c oxidase activity;P:unknown;C:mitochondrion;MPOO.I.H.G.S.X.
0.4152.40.89At2g20820816613unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.4050.80.87At1g27530839644-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPO.I.H.G.S.X.
0.4050.80.88At3g52730824439ubiquinol-cytochrome C reductase UQCRX/QCR9-like family proteinF:ubiquinol-cytochrome-c reductase activity;P:mitochondrial electron transport, ubiquinol to cytochrome c;C:mitochondrial envelope, mitochondrion, mitochondrial respiratory chain complex III, membrane;PFMOO.I.H.G.S.X.
0.3948.40.87At5g10980830965histone H3F:DNA binding;P:nucleosome assembly;C:nucleus, nucleosome;MFPOO.I.H.G.S.X.
0.3643.60.87At1g19130838496-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOPFAMO.I.H.G.S.X.
0.3643.60.88At1g49140841337NADH-ubiquinone oxidoreductase-relatedF:unknown;P:photorespiration;C:mitochondrion, mitochondrial membrane, respiratory chain complex I;FPMO.I.H.G.S.X.
0.3541.60.87At5g53560835438CB5-E (CYTOCHROME B5 ISOFORM E)Encodes a cytochrome b5 isoform that can be reduced by AtCBR, a cytochrome b5 reductase.O.I.H.G.S.X.
0.3541.60.88At4g00860826213ATOZI1putative pathogenesis-related protein whose transcript level is induced in response to ozone and pathogenic Pseudomonas strains.O.I.H.G.S.X.
0.3439.80.87At5g64400836561-F:molecular_function unknown;P:biological_process unknown;C:unknown;MFPOBO.I.H.G.S.X.
0.3338.10.89At2g04900815037unknown proteinF:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;BOMPFO.I.H.G.S.X.
0.3338.10.87At4g34700829622complex 1 family protein / LVR family proteinF:catalytic activity;P:photorespiration;C:mitochondrial membrane, plasma membrane, respiratory chain complex I;MFPOO.I.H.G.S.X.
0.3338.10.87At2g47380819351cytochrome c oxidase subunit Vc family protein / COX5C family proteinF:cytochrome-c oxidase activity;P:unknown;C:mitochondrion;PO.I.H.G.S.X.
0.3235.70.87At5g47570834807unknown proteinF:molecular_function unknown;P:biological_process unknown;C:respiratory chain complex I;POO.I.H.G.S.X.
0.3235.70.89At1g22840838889CYTC-1 (CYTOCHROME C-1)Encodes cytochrome c. Contains two site II (TGGGCC/T) elements, which interact with a TCP-domain transcription factor, and a downstream internal telomeric repeat, and are required for expression of the Cytc-1 gene. Promoter directs preferential expression in root and shoot meristems and in anthers.O.I.H.G.S.X.
0.3235.70.88At5g67590836895FRO1 (FROSTBITE1)Mutant leaves have a reduced capacity for cold acclimation, appear water-soaked, leak electrolytes, and accumulate reactive oxygen species constitutively. Encode a protein with high similarity to the 18-kD Fe-S subunit of complex I (NADH dehydrogenase, EC 1.6.5.3) in the mitochondrial electron transfer chain.O.I.H.G.S.X.
0.3235.70.87At4g15940827276fumarylacetoacetate hydrolase family proteinF:catalytic activity;P:metabolic process;C:mitochondrion;BOFMAPO.I.H.G.S.X.
0.3032.10.86At4g32470829382ubiquinol-cytochrome C reductase complex 14 kDa protein, putativeF:ubiquinol-cytochrome-c reductase activity;P:mitochondrial electron transport, ubiquinol to cytochrome c;C:mitochondrion, plasma membrane, plastid, mitochondrial respiratory chain complex III, membrane;MPFOO.I.H.G.S.X.
0.3032.10.88At5g47200834766ATRAB1AF:GTP binding;P:protein transport, small GTPase mediated signal transduction;C:plasma membrane;MOFPBVAO.I.H.G.S.X.
0.3032.10.86At2g03680814896SPR1 (SPIRAL1)The SPR1 gene encodes a plant-specific 12-kD protein which has a repeated motif at both ends, separated by a predicted rod-like domain, suggesting that it may act as an intermolecular linker. Ubiquitously expressed and belongs to a six-member gene family in Arabidopsis; expressed in transgenic seedlings localized to microtubules within the cortical array, preprophase band, phragmoplast, and mitotic spindle.O.I.H.G.S.X.
0.2930.30.86At5g41560834158-F:molecular_function unknown;P:biological_process unknown;C:chloroplast;MPO.I.H.G.S.X.
0.2930.30.88At3g023608211636-phosphogluconate dehydrogenase family proteinF:in 6 functions;P:response to salt stress;C:peroxisome;BOMPFAVO.I.H.G.S.X.
0.2930.30.87At3g09810820139isocitrate dehydrogenase, putative / NAD+ isocitrate dehydrogenase, putativeF:isocitrate dehydrogenase (NAD+) activity, oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;P:tricarboxylic acid cycle, metabolic process;C:mitochondrion;BOMFAPO.I.H.G.S.X.
0.2930.30.87At4g322103770570SDH3-2Encodes one of the membrane anchor subunits of the mitochondrial respiratory complex II. The protein is encoded by the nuclear genome but is imported into the mitochondrion. There are two genes that encode this protein, the other is SDH3-1.O.I.H.G.S.X.
0.2930.30.88At5g50850835157MAB1 (MACCI-BOU)F:pyruvate dehydrogenase (acetyl-transferring) activity, catalytic activity;P:defense response to bacterium;C:mitochondrion, nucleolus, plasma membrane;BOMPFAO.I.H.G.S.X.
0.2930.30.86At5g64350836556FKBP12 (FK506-BINDING PROTEIN)F:FK506 binding, peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:chloroplast thylakoid lumen;BMOFPAO.I.H.G.S.X.
0.2930.30.86At1g65930842905isocitrate dehydrogenase, putative / NADP+ isocitrate dehydrogenase, putativeF:isocitrate dehydrogenase (NADP+) activity, copper ion binding;P:response to cadmium ion, response to salt stress, metabolic process;C:apoplast, plasma membrane;OBMPFAO.I.H.G.S.X.
0.2930.30.89At3g48140823969senescence-associated protein, putativeF:molecular_function unknown;P:leaf senescence;C:endomembrane system;PO.I.H.G.S.X.
0.2930.30.86At3g52300824395ATPQ (ATP SYNTHASE D CHAIN, MITOCHONDRIAL)F:hydrogen ion transmembrane transporter activity;P:response to salt stress;C:in 8 components;MPFOO.I.H.G.S.X.
0.2930.30.87At2g38130818391ATMAK3Encodes the Arabidopsis homolog of the yeast protein MAK3, a component of the N-terminal acetyltransferase complex C. In mutant plants, synthesis of plastome-encoded photosystem II core proteins D1 and CP47 is affected resulting in fewer thylakoid multiprotein complexes.O.I.H.G.S.X.
0.2726.20.87At2g44525819060unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;BMOFPO.I.H.G.S.X.
0.2726.20.87At4g29480829069mitochondrial ATP synthase g subunit family proteinF:hydrogen ion transmembrane transporter activity;P:proton transport, ATP synthesis coupled proton transport;C:mitochondrion;POO.I.H.G.S.X.
0.2624.40.87At4g22310828326unknown proteinF:unknown;P:biological_process unknown;C:mitochondrion;MFPOO.I.H.G.S.X.
0.2420.70.87At3g62580825432-F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MFPBO.I.H.G.S.X.
0.2420.70.87At4g051608258644-coumarate--CoA ligase, putative / 4-coumaroyl-CoA synthase, putativeEncodes a peroxisomal protein involved in the activation of fatty acids through esterification with CoA. At4g05160 preferentially activates fatty acids with medium chain length (C6:0 and C7:0) as well as even-numbered long-chain fatty acids (C14:0, C16:0 and C18:0). At4g05160 was also able to catalyze the conversion of OPC-6:0 to its CoA ester and is therefore thought to be involved in the peroxisomal β-oxidation steps of jasmonic acid biosynthesis.O.I.H.G.S.X.
0.2319.30.86At3g18430821372calcium-binding EF hand family proteinF:calcium ion binding;P:N-terminal protein myristoylation;C:vacuole;MPOFBO.I.H.G.S.X.
0.2217.50.86At3g04780819638-Encodes a protein with little sequence identity with any other protein of known structure or function. Part of this protein shows a 42% sequence identity with the C-terminal domain of the 32-kD human thioredoxin-like protein.O.I.H.G.S.X.
0.2217.50.87At4g23650828465CDPK6 (CALCIUM-DEPENDENT PROTEIN KINASE 6)Encodes calcium dependent protein kinase 3 (CPK3), a member of the Arabidopsis CDPK gene family. CDPKs contain an intrinsic Ca2+-activation domain with four EF hand Ca2+-binding sites. CDPKs protein kinases have been proposed to function in multiple plant signal transduction pathways downstream of [Ca2+]cyt elevations, thus transducing various physiological responses. CPK3 is expressed in both guard cells and mesophyll cells. Functions in guard cell ion channel regulation. ABA and Ca(2+) activation of slow-type anion channels and, interestingly, ABA activation of plasma membrane Ca(2+)-permeable channels were impaired in independent alleles of single and double cpk3cpk6 mutant guard cells. Furthermore, ABA- and Ca(2+)-induced stomatal closing were partially impaired in these cpk3cpk6 mutant alleles. CPK6 is also a member of the Arabidopsis CDPK family.O.I.H.G.S.X.
0.2217.50.87At1g69960843333PP2A (SERINE/THREONINE PROTEIN PHOSPHATASE 2A)type 2A serine/threonine protein phosphatase (PP2A) mRNA,O.I.H.G.S.X.
0.2014.40.86At4g07390826170PQ-loop repeat family protein / transmembrane family proteinF:unknown;P:unknown;C:membrane;MPFOO.I.H.G.S.X.
0.1912.70.87At1g28280839722VQ motif-containing proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PMFOBO.I.H.G.S.X.
0.1811.40.89At5g03290831884isocitrate dehydrogenase, putative / NAD+ isocitrate dehydrogenase, putativeF:isocitrate dehydrogenase (NAD+) activity, ATP binding;P:tricarboxylic acid cycle, metabolic process;C:mitochondrion, chloroplast;BOMFAPO.I.H.G.S.X.
0.1710.20.87At1g09920837524TRAF-type zinc finger-relatedF:zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MOFPO.I.H.G.S.X.
0.1710.20.87At1g21380838737VHS domain-containing protein / GAT domain-containing proteinF:protein transporter activity;P:intracellular protein transport, intra-Golgi vesicle-mediated transport;C:Golgi stack, intracellular;MFPOBO.I.H.G.S.X.
0.1710.20.86At5g08290830725YLS8Encodes Dim1 homolog.O.I.H.G.S.X.
0.146.80.87At3g58600825029-F:molecular_function unknown;P:endocytosis;C:membrane;MPFOO.I.H.G.S.X.
0.124.90.86At1g04960839346-F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PBOO.I.H.G.S.X.
0.092.80.87At2g45140819122PVA12 (PLANT VAP HOMOLOG 12)Encodes a Plant VAMP-Associated protein that localizes to the ER and binds to the sitosterol-binding protein ORP3a. The WFDE motif in ORP3a appears to be important for this direct interaction. Mutation of this motif causes ORP3a to relocalize to the Golgi and cytosol. The interaction between PVA12 and ORP3a does not appear to be sterol-dependent.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
47.099.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
39.799.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.499.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.499.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.899.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.399.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.099.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.999.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.999.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.699.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.499.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.499.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.399.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.199.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.199.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.999.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.399.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.299.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.799.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.199.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.399.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.199.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.499.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.499.6GSM258003LMPC-derived phloem_2GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO
22.599.6GSM258002LMPC-derived phloem_1GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO
17.599.5GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.899.5GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.599.3E-MEXP-1725-raw-cel-1669614634
12.299.3GSM133761Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.599.3GSM258004LMPC-derived phloem_3GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO
11.599.3E-MEXP-1725-raw-cel-1669614562
10.999.2GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.399.2E-MEXP-1725-raw-cel-1669614623
10.299.2E-MEXP-98-raw-cel-320188914
9.399.1GSM284384Arabidopsis GEP5GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.399.1E-ATMX-35-raw-cel-1574334832
9.299.1E-MEXP-1451-raw-cel-1585200202
9.199.1GSM284385Arabidopsis GEP6GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.099.1GSM311293Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
8.999.0GSM133966Fukuda_1-11_10A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
8.999.0E-MEXP-1451-raw-cel-1585200266
8.999.0GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0662GO:0006122The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.Link to AmiGO
0.0552GO:0006099A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.Link to AmiGO
0.0452GO:0009853A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.081800190Oxidative phosphorylationLink to KEGG PATHWAY
0.068400020Citrate cycle (TCA cycle)Link to KEGG PATHWAY
0.055300480Glutathione 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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