Co-expression analysis

Gene ID At5g63680
Gene name pyruvate kinase, putative
Module size 54 genes
NF 0.23
%ile 23.9

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
1.00100.01.00At5g63680836488pyruvate kinase, putativeF:pyruvate kinase activity, potassium ion binding, magnesium ion binding, catalytic activity;P:response to cadmium ion, glycolysis;C:plasma membrane;BOMPFAO.I.H.G.S.X.
0.4558.30.90At3g52200824385LTA3dihydrolipoamide S-acetyltransferase (LTA3) mRNA, nuclearO.I.H.G.S.X.
0.3745.00.88At1g51980841627mitochondrial processing peptidase alpha subunit, putativeF:metalloendopeptidase activity, ATP binding;P:proteolysis, response to salt stress;C:in 6 components;BOMFPAVO.I.H.G.S.X.
0.3643.60.89At3g49390824101CID10RNA-binding protein, putative, RNA-binding protein RBP37, Arabidopsis thaliana, PIR:T04196.Member of a family of PAB2 domain containing proteins.O.I.H.G.S.X.
0.3541.60.89At3g17240820984mtLPD2 (LIPOAMIDE DEHYDROGENASE 2)lipoamide dehydrogenase precursorO.I.H.G.S.X.
0.3439.80.89At1g53310841765ATPPC1 (PHOSPHOENOLPYRUVATE CARBOXYLASE 1)Encodes one of four Arabidopsis phosphoenolpyruvate carboxylase proteins.O.I.H.G.S.X.
0.3235.70.89At2g16950816198TRN1 (TRANSPORTIN 1)Nuclear import receptor for AtGRP7.O.I.H.G.S.X.
0.3133.80.88At3g554108247072-oxoglutarate dehydrogenase E1 component, putative / oxoglutarate decarboxylase, putative / alpha-ketoglutaric dehydrogenase, putativeF:oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor, oxoglutarate dehydrogenase (succinyl-transferring) activity, thiamin pyrophosphate binding;P:glycolysis, metabolic process;C:mitochondrion;OBMFPAO.I.H.G.S.X.
0.3032.10.88At2g20760816605protein binding / structural moleculeF:protein binding, structural molecule activity;P:intracellular protein transport, vesicle-mediated transport;C:plasma membrane;MBOPFO.I.H.G.S.X.
0.3032.10.89At2g17980816310ATSLY1member of SLY1 Gene FamilyO.I.H.G.S.X.
0.2930.30.89At3g48170823972ALDH10A9Arabidopsis thaliana putative betaine aldehyde dehydrogenaseO.I.H.G.S.X.
0.2930.30.88At5g03290831884isocitrate 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.
0.2930.30.88At5g58290835941RPT3 (REGULATORY PARTICLE TRIPLE-A ATPASE 3)26S proteasome AAA-ATPase subunit RPT3 (RPT3) mRNA,O.I.H.G.S.X.
0.2930.30.88At1g71860843516PTP1 (PROTEIN TYROSINE PHOSPHATASE 1)Encodes a protein with tyrosine phosphatase activity that is downregulated in response to cold and upregulated in response to salt stress.O.I.H.G.S.X.
0.2930.30.88At2g259108171323'-5' exonuclease domain-containing protein / K homology domain-containing protein / KH domain-containing proteinF:3'-5' exonuclease activity, RNA binding, nucleic acid binding;P:nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;C:intracellular;BOMPFO.I.H.G.S.X.
0.2830.30.89At2g44100819016ATGDI1 (ARABIDOPSIS THALIANA GUANOSINE NUCLEOTIDE DIPHOSPHATE DISSOCIATION INHIBITOR 1)GDP dissociation inhibitor involved in vesicular membrane trafficO.I.H.G.S.X.
0.2726.20.88At4g04910825830NSF (N-ethylmaleimide sensitive factor)N-ethylmaleimide sensitive factorO.I.H.G.S.X.
0.2726.20.90At2g20420816561succinyl-CoA ligase (GDP-forming) beta-chain, mitochondrial, putative / succinyl-CoA synthetase, beta chain, putative / SCS-beta, putativeF:succinate-CoA ligase (GDP-forming) activity, ATP binding;P:response to cadmium ion, metabolic process;C:mitochondrion;OBMFAPO.I.H.G.S.X.
0.2624.40.87At5g550708355982-oxoacid dehydrogenase family proteinF:dihydrolipoyllysine-residue succinyltransferase activity, acyltransferase activity;P:response to oxidative stress, metabolic process;C:cytosolic ribosome, mitochondrion;BOMPFVAO.I.H.G.S.X.
0.2624.40.88At3g06720819857IMPA-1 (IMPORTIN ALPHA ISOFORM 1)Encodes importin alpha involved in nuclear import. Protein interacts with Agrobacterium proteins VirD2 and VirE2. Is not individually essential for Agrobacterium-mediated root transformation, but when overexpressed can rescue the impa-4 decreased transformation susceptibility phenotype.O.I.H.G.S.X.
0.2624.40.88At3g02090821084mitochondrial processing peptidase beta subunit, putativeF:metalloendopeptidase activity, catalytic activity, zinc ion binding, metal ion binding;P:proteolysis;C:in 11 components;BOMFPAVO.I.H.G.S.X.
0.2624.40.87At5g64440836565AtFAAH (Arabidopsis thaliana fatty acid amide hydrolase)AtFAAH (fatty acid amide hydrolase) modulates endogenous NAEs (N-Acylethanolamines) levels in plants by hydrolyzing NAEs to ethanolamine and their corresponding free fatty acids. NAE depletion likely participates in the regulation of plant growth.O.I.H.G.S.X.
0.2522.60.87At3g53110824477LOS4 (LOW EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 4)Encodes a putative DEAD-Box RNA Helicase and has RNA-dependent ATPase activity. Mutant is Sensitive to chilling stress and heat stress. Germination of the mutant is inhibited by ABA. LOS4 may be involved in temperature sensing. Is enriched in the nuclear envelope and also located in the cytoplasm. LOS4 is involved in export of poly A RNA.O.I.H.G.S.X.
0.2522.60.88At5g37510833729EMB1467 (embryo defective 1467)Encodes a subunit of the 400 kDa subcomplex of the mitochondrial NADH dehydrogenase (complex I). The protein has been isolated in the male gametophyte.O.I.H.G.S.X.
0.2420.70.88At5g38830833874tRNA synthetase class I (C) family proteinF:cysteine-tRNA ligase activity, nucleotide binding, ATP binding;P:response to cadmium ion, cysteinyl-tRNA aminoacylation;C:cytoplasm;OBMFAPVO.I.H.G.S.X.
0.2319.30.87At2g21270816666ubiquitin fusion degradation UFD1 family proteinF:molecular_function unknown;P:ubiquitin-dependent protein catabolic process;C:unknown;OFMPABO.I.H.G.S.X.
0.2319.30.89At2g21870816723unknown proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion, nucleolus, chloroplast, plastid, membrane;PMOBAO.I.H.G.S.X.
0.2319.30.88At2g27020817244PAG1Encodes 20S proteasome subunit PAG1 (PAG1).O.I.H.G.S.X.
0.2217.50.88At1g22300838837GRF10 (GENERAL REGULATORY FACTOR 10)Encodes a 14-3-3 protein. This protein is reported to interact with the BZR1 transcription factor involved in brassinosteroid signaling and may affect the nucleocytoplasmic shuttling of BZR1O.I.H.G.S.X.
0.2217.50.88At1g20110838600zinc finger (FYVE type) family proteinF:phosphoinositide binding;P:signal transduction;C:unknown;MFOPBVAO.I.H.G.S.X.
0.2217.50.88At2g21520816691transporterF:transporter activity;P:transport;C:intracellular;MPFOO.I.H.G.S.X.
0.2115.80.88At5g51430835217EYE (EMBRYO YELLOW)Encodes a protein that is homologous to Cog7, a subunit of the conserved oligomeric Golgi (COG) complex, which is required for the normal morphology and function of the Golgi apparatus. It is likely to be involved in transport or retention of Golgi-localized proteins and in maintenance of Golgi morphology.O.I.H.G.S.X.
0.2115.80.88At2g24200816954cytosol aminopeptidaseF:manganese ion binding, metalloexopeptidase activity, aminopeptidase activity;P:response to cadmium ion, proteolysis;C:vacuole;OBMPFAO.I.H.G.S.X.
0.2115.80.88At3g05530819718RPT5A (REGULATORY PARTICLE TRIPLE-A ATPASE 5A)Encodes RPT5a (Regulatory Particle 5a), one of the six AAA-ATPases of the proteasome regulatory particle. Essential for gametophyte development. In Arabidopsis, the RPT5 subunit is encoded by two highly homologous genes, RPT5a and RPT5b. RPT5a and RPT5b show accession-dependent functional redundancy. In Wassilewskija (Ws) accession: mutant alleles of RPT5a displayed 50% pollen lethality, indicating that RPT5a is essential for male gametophyte development. In the Columbia (Col) accession, a rpt5a mutant allele did not display such a phenotype because the RPT5b Col allele complements the rpt5a defect in the male gametophyte, whereas the RPT5b Ws allele does not. Double rpt5a rpt5b mutants in Col background showed a complete male and female gametophyte lethal phenotype.O.I.H.G.S.X.
0.2115.80.87At2g45140819122PVA12 (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.
0.2014.40.88At1g27000839590bZIP family transcription factorF:DNA binding;P:regulation of transcription, DNA-dependent;C:unknown;POBMO.I.H.G.S.X.
0.2014.40.88At2g25280817066-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BAMOFPO.I.H.G.S.X.
0.1912.70.88At1g05520837054transport protein, putativeF:protein binding, transporter activity, zinc ion binding;P:transport, response to salt stress;C:COPII vesicle coat;MFOPO.I.H.G.S.X.
0.1912.70.88At3g02520821060GRF7 (GENERAL REGULATORY FACTOR 7)Encodes GF14 ν, a 14-3-3 protein isoform (14-3-3ν).O.I.H.G.S.X.
0.1811.40.87At1g47420841147-F:molecular_function unknown;P:biological_process unknown;C:mitochondrion, nucleus;POO.I.H.G.S.X.
0.1811.40.88At5g13430831184ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial, putative / Rieske iron-sulfur protein, putativeF:metal ion binding;P:oxidation reduction;C:mitochondrion, mitochondrial respiratory chain complex III, membrane;OBPMFAO.I.H.G.S.X.
0.1811.40.88At1g25280839112AtTLP10 (TUBBY LIKE PROTEIN 10)Member of TLP familyO.I.H.G.S.X.
0.1811.40.88At5g49830835046-F:unknown;P:unknown;C:plasma membrane;MFPOVO.I.H.G.S.X.
0.1811.40.88At4g31480829275coatomer beta subunit, putative / beta-coat protein, putative / beta-COP, putativeF:protein binding, clathrin binding, structural molecule activity, binding;P:intracellular protein transport, vesicle-mediated transport;C:membrane coat, endomembrane system, COPI vesicle coat;MOFPO.I.H.G.S.X.
0.1710.20.88At4g17270827441Mo25 family proteinF:binding;P:biological_process unknown;C:plasma membrane;MFPOO.I.H.G.S.X.
0.1710.20.87At5g52240835300MSBP1 (membrane steroid binding protein 1)Encodes a protein with similarity to progesterone-binding proteins in animals. Has been shown to bind steroids in vitro. Expressed in aerial portions of the plant excluding mature flowers and siliques. Antisense experiments suggest a role in inhibition of hypocotyl cell elongation. Expression is suppressed light grown seedlings transferred to the dark.O.I.H.G.S.X. protein complex, subunit alpha, putativeF:protein binding, structural molecule activity, transporter activity;P:intracellular protein transport, vesicle-mediated transport, ER to Golgi vesicle-mediated transport;C:COPI vesicle coat, CUL4 RING ubiquitin ligase complex, membrane;MFOBPAO.I.H.G.S.X. CA3 (GAMMA CARBONIC ANHYDRASE 3)Encodes mitochondrial gamma carbonic anhydrase. Component of the NADH dehydrogenase complex.O.I.H.G.S.X. transporter CorA-like family protein (MRS2-3)F:metal ion transmembrane transporter activity;P:metal ion transport;C:plasma membrane, membrane;PFMOBO.I.H.G.S.X., putativeF:protein transporter activity, protein binding, clathrin binding, binding;P:intracellular protein transport, vesicle-mediated transport, protein transport;C:plasma membrane;MFOPBAO.I.H.G.S.X. repeat (TPR)-containing proteinF:binding;P:unknown;C:cellular_component unknown;MOPFBAVO.I.H.G.S.X. protein-relatedF:molecular_function unknown;P:biological_process unknown;C:chloroplast;PVAOFMO.I.H.G.S.X. a member of the exportin protein family (XPO1A) which functions as receptors for nuclear export. Binds to a variety of proteins having leucine rich export signals.Along with XPO1B involved with development of the male and female gametophytes.O.I.H.G.S.X. family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAVO.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
81.399.9GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
80.099.9GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
78.799.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
72.299.9GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
67.699.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
67.299.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
67.199.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
65.899.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
65.499.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
63.199.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
62.699.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
62.599.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
60.399.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
60.099.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
59.899.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
59.299.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
58.499.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
57.899.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
57.899.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
57.599.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
57.199.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
55.599.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
52.899.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
52.299.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.299.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.599.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
28.799.7GSM142738DH001_ATH1_A5-BCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
28.499.7GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
24.599.6GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
22.599.6GSM311278Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
22.499.6GSM284391Arabidopsis GPE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
20.899.6GSM142737DH001_ATH1_A4-UNM2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
20.299.6GSM142734DH001_ATH1_A1-UNM1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
17.699.5GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
17.299.5GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
15.699.5GSM284390Arabidopsis GPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
15.099.4GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
14.899.4GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.599.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.399.3GSM311277Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0582GO:0000059The aggregation, arrangement and bonding together of the nuclear localization signal of a protein with nuclear envelope proteins such as importins.Link to AmiGO
0.0585GO:0016192The directed movement of substances into, out of or within a cell by a cellular process that begins with the formation of membrane-bounded vesicles in which the transported substances are enclosed or located in the vesicle membrane. Vesicles are then targeted to, and fuse with, an acceptor membrane.Link to AmiGO
0.0562GO: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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.104600020Citrate cycle (TCA cycle)Link to KEGG PATHWAY
0.067701066Biosynthesis of alkaloids derived from terpenoid and polyketideLink to KEGG PATHWAY
0.067400620Pyruvate metabolismLink to KEGG PATHWAY

Inter-species module comparison

Select a plant to compare co-expressed genes between species.

Back to the CoP portal site

Back to the KAGIANA project homepage