Co-expression analysis

Gene ID At3g08950
Gene name electron transport SCO1/SenC family protein
Module size 62 genes
NF 0.20
%ile 19.1



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
0.9597.01.00At3g08950820046electron transport SCO1/SenC family proteinF:copper ion binding;P:copper ion transport, respiratory chain complex IV assembly, cellular copper ion homeostasis, cell redox homeostasis;C:mitochondrion, plastid;BOMFPAO.I.H.G.S.X.
0.4152.40.88At3g17910821310SURF1 (SURFEIT 1)Surfeit 1 (SURF1) mRNA. Similar to human SURF1 which is known to be involved in cytochrome c oxidase assembly.O.I.H.G.S.X.
0.4152.40.88At1g08220837343-F:molecular_function unknown;P:mitochondrial proton-transporting ATP synthase complex assembly;C:mitochondrial inner membrane;FPOAMO.I.H.G.S.X.
0.3338.10.89At4g29830829105VIP3 (vernalization independence 3)The protein is composed of repeats of WD motif which is involved in protein complex formation. The gene is involved in flower timing and flower development. This gene is predicted to encode a protein with a DWD motif. It can bind to DDB1a in Y2H assays, and DDB1b in co-IP assays, and may be involved in the formation of a CUL4-based E3 ubiquitin ligase. Loss of gene function leads to a redistribution of H3K4me3 and K3K36me2 modifications within genes but not a change in the overall abundance of these modifications within chromatin.O.I.H.G.S.X.
0.3032.10.88At1g61990842494mitochondrial transcription termination factor-related / mTERF-relatedF:molecular_function unknown;P:biological_process unknown;C:unknown;PMOO.I.H.G.S.X.
0.2930.30.89At2g26590817200adhesion regulating molecule familyF:molecular_function unknown;P:cell adhesion;C:integral to membrane, nucleus, cytoplasm;MOFPO.I.H.G.S.X.
0.2930.30.89At5g23250832389succinyl-CoA ligase (GDP-forming) alpha-chain, mitochondrial, putative / succinyl-CoA synthetase, alpha chain, putative / SCS-alpha, putativeF:succinate-CoA ligase (ADP-forming) activity, succinate-CoA ligase (GDP-forming) activity, binding, ATP citrate synthase activity, catalytic activity;P:metabolic process;C:mitochondrion;OBMAFPO.I.H.G.S.X.
0.2830.30.88At2g35720818142DNAJ heat shock N-terminal domain-containing proteinF:heat shock protein binding;P:protein folding;C:mitochondrion, plastid;BOMFPAVO.I.H.G.S.X.
0.2830.30.88At1g22920838899CSN5A (COP9 SIGNALOSOME 5A)AJH1 encodes a protein similar to JAB1, a specific mammalian coactivator of AP-1 transcription. Encodes a subunit of the COP9 complex that is involved in protein deneddylation. Plants with mutations in CSN5A and CSN5B have a de-etiolated phenotype.O.I.H.G.S.X.
0.2830.30.89At2g31240817681tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;MBOFPAVO.I.H.G.S.X.
0.2830.30.88At3g15010820730RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:unknown;C:nucleolus;MBPOFVAO.I.H.G.S.X.
0.2726.20.88At3g61620825335RRP41exonuclease RRP41 (RRP41)O.I.H.G.S.X.
0.2624.40.88At1g34130840312STT3B (staurosporin and temperature sensitive 3-like b)Encodes homolog of yeast STT3, a subunit of oligosaccharyltransferase.O.I.H.G.S.X.
0.2624.40.88At3g26410822245methyltransferase/ nucleic acid bindingF:methyltransferase activity, nucleic acid binding;P:methylation;C:endomembrane system;MAFOPBO.I.H.G.S.X.
0.2624.40.88At3g077508199663' exoribonuclease family domain 1-containing proteinF:3'-5'-exoribonuclease activity, RNA binding;P:RNA processing;C:cellular_component unknown;MOFAPBO.I.H.G.S.X.
0.2522.60.88At4g35910829746unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOAO.I.H.G.S.X.
0.2522.60.89At4g2362082846250S ribosomal protein-relatedF:structural constituent of ribosome, 5S rRNA binding;P:translation;C:ribosome, intracellular;OBPO.I.H.G.S.X.
0.2522.60.88At5g40530834051-F:unknown;P:unknown;C:unknown;MOFPO.I.H.G.S.X.
0.2420.70.88At1g45332841097mitochondrial elongation factor, putativeF:translation factor activity, nucleic acid binding, translation elongation factor activity, ATP binding;P:translational elongation;C:mitochondrion;BOMFPAO.I.H.G.S.X.
0.2420.70.88At4g02930828134elongation factor Tu, putative / EF-Tu, putativeF:translation elongation factor activity, ATP binding;P:translational elongation;C:mitochondrion, cell wall;BOMFPAVO.I.H.G.S.X.
0.2420.70.88At5g22840832347protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.2420.70.88At2g34260817987transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MBFOPAO.I.H.G.S.X.
0.2319.30.88At1g04190839442tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;OBMPFAO.I.H.G.S.X.
0.2217.50.88At3g12180820395cornichon family proteinF:molecular_function unknown;P:intracellular signaling cascade;C:endomembrane system, membrane;MFPOO.I.H.G.S.X.
0.2217.50.88At1g73240843658unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO.I.H.G.S.X.
0.2217.50.88At1g65650842876UCH2F:ubiquitin-specific protease activity, ubiquitin thiolesterase activity;P:protein deubiquitination, shoot development, shoot morphogenesis, leaf development, ubiquitin-dependent protein catabolic process;C:nucleus, intracellular, cytoplasm;MFOPO.I.H.G.S.X.
0.2217.50.88At5g50840835156-F:unknown;P:biological_process unknown;C:unknown;MOBFPAVO.I.H.G.S.X.
0.2115.80.88At4g31180829246aspartyl-tRNA synthetase, putative / aspartate--tRNA ligase, putativeF:aspartate-tRNA ligase activity, nucleotide binding, aminoacyl-tRNA ligase activity, nucleic acid binding, ATP binding;P:response to cadmium ion, aspartyl-tRNA aminoacylation;C:chloroplast, cytoplasm;BOMFAPO.I.H.G.S.X.
0.2115.80.88At3g02650821285pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.2115.80.88At4g26900828797AT-HF (HIS HF)encodes a glutamine amidotransferase and cyclase, catalyzes the fifth and sixth steps of the histidine biosynthetic pathwayO.I.H.G.S.X.
0.2014.40.88At5g48030834854GFA2 (GAMETOPHYTIC FACTOR 2)encodes a mitochondrially targeted DNAJ protein involved in female gametophyte development.O.I.H.G.S.X.
0.2014.40.88At1g26460839187pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion;POFMO.I.H.G.S.X.
0.2014.40.88At2g25570817096bindingF:binding;P:biological_process unknown;C:unknown;BOMPVFO.I.H.G.S.X.
0.2014.40.87At5g05000830382TOC34 (TRANSLOCON AT THE OUTER ENVELOPE MEMBRANE OF CHLOROPLASTS 34)Outer membrane protein that may function in import of nuclear encoded proteins into the chloroplast.O.I.H.G.S.X.
0.2014.40.88At5g26710832718glutamate-tRNA ligase, putative / glutamyl-tRNA synthetase, putatuve / GluRS, putativeF:glutamate-tRNA ligase activity;P:glutamyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:cytoplasm;BOMFAPO.I.H.G.S.X.
0.1912.70.87At1g05055839332GTF2H2 (GENERAL TRANSCRIPTION FACTOR IIH 2)Member of transcription factor TFIIH complex. Involved in transcription and DNA repair and interacts with AtXPD.O.I.H.G.S.X.
0.1811.40.88At2g20810816611GAUT10 (GALACTURONOSYLTRANSFERASE 10)Encodes a protein with putative galacturonosyltransferase activity.O.I.H.G.S.X.
0.1811.40.88At3g14290820649PAE2Encodes 20S proteasome subunit PAE2 (PAE2).O.I.H.G.S.X.
0.1811.40.88At1g16870838258mitochondrial 28S ribosomal protein S29-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPO.I.H.G.S.X.
0.1811.40.88At1g13060837863PBE1Encodes 20S proteasome beta subunit PBE1 (PBE1).O.I.H.G.S.X.
0.1811.40.88At1g25380839124mitochondrial substrate carrier family proteinF:transporter activity, binding;P:transport, mitochondrial transport;C:mitochondrial inner membrane, membrane;MFPOVO.I.H.G.S.X.
0.1811.40.88At1g67490843070GCS1 (GLUCOSIDASE 1)Encodes an alpha-glucosidase I enzyme that catalyzes the first step in N-linked glycan processing. Localized to the endoplasmic reticulum (ER).O.I.H.G.S.X.
0.1811.40.90At5g56730835774peptidase M16 family protein / insulinase family proteinF:metalloendopeptidase activity, catalytic activity, zinc ion binding, metal ion binding;P:proteolysis;C:mitochondrion, chloroplast, plastid;BOMFPAVO.I.H.G.S.X.
0.1710.20.88At2g43770818980transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAVO.I.H.G.S.X.
0.1710.20.87At3g18860821419transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:cellular_component unknown;MFOBPAO.I.H.G.S.X.
0.1710.20.88At3g57290824896EIF3E (EUKARYOTIC TRANSLATION INITIATION FACTOR 3E)Encodes a protein that is found in not only the eif3 complex but also in association with subunits of the COP9 signalosome. eIF3e appears to be subjected to proteasome-dependent degradation that requires the PCI domain of eIF3e. The level of eIF3e present in cells appears to affect the rate of translation.O.I.H.G.S.X.
0.1710.20.88At5g64730836594transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;MFOBPAVO.I.H.G.S.X.
0.1710.20.88At5g19690832089STT3A (STAUROSPORIN AND TEMPERATURE SENSITIVE 3-LIKE A)encodes an oligosaccharyl transferase involved response to high salt. Mutants are hypersensitive to high salt conditionsO.I.H.G.S.X.
0.1710.20.88At5g62050836325OXA1essential factor for protein sorting and assembly into membranesO.I.H.G.S.X.
0.168.80.88At5g27540832814MIRO1 (Miro-related GTP-ase 1)Encodes a protein with similarity to GTPases that is localized to the mitochondrion. Involved in embryogenesis, pollen tube growth and required for mitochondrial development.O.I.H.G.S.X.
0.168.80.89At1g64520842760RPN12a (Regulatory Particle non-ATPase 12a)F:peptidase activity;P:in 14 processes;C:proteasome complex, nucleus, proteasome regulatory particle, lid subcomplex, chloroplast envelope;MFOPO.I.H.G.S.X.
0.168.80.88At4g39920830151POR (PORCINO)Microtubule-folding cofactor, produces assembly-competent alpha-/beta-tubulin heterodimers.O.I.H.G.S.X.
0.157.80.89At2g35790818151unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MPFOO.I.H.G.S.X.
0.157.80.87At4g19210827661ATRLI2member of RLI subfamilyO.I.H.G.S.X.
0.146.80.89At1g19240838507unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.146.80.88At1g26750839216unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.135.80.89At5g05920830477DHS (DEOXYHYPUSINE SYNTHASE)Encodes a deoxyhypusine synthase.O.I.H.G.S.X.
0.124.90.87At1g43690840956ubiquitin interaction motif-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPO.I.H.G.S.X.
0.114.10.88At1g13180837876DIS1 (DISTORTED TRICHOMES 1)Mutant has defect in trichome cell expansion and actin organization resulting in a distorted trichome phenotype.O.I.H.G.S.X.
0.114.10.88At5g51510835225unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.114.10.87At4g39220830077ATRER1AKey player of retrieval of ER membrane proteinsO.I.H.G.S.X.
0.082.30.88At1g13870837946DRL1 (DEFORMED ROOTS AND LEAVES 1)Encodes a homolog of the yeast TOT4/KTI12 protein. Yeast TOT4/KTI12 associates with Elongator, a multisubunit complex that binds the RNA polymerase II transcription elongation complex. Ds insertion mutant has enlarged shoot apical region, 4 to 6 long slender leaves followed by spike-like structures, short roots.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
65.499.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
47.999.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
40.199.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.299.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.099.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.199.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.099.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.699.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.599.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.499.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.199.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.699.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.599.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.199.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.899.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
31.599.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.899.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.599.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.699.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.899.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.299.6GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.999.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.799.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.599.6GSM133761Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
16.499.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.899.4GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.099.4GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.599.3GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
8.799.0GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0572GO:0008535The aggregation, arrangement and bonding together of a set of components to form respiratory chain complex IV (also known as cytochrome c oxidase), the terminal member of the respiratory chain of the mitochondrion and some aerobic bacteria. Cytochrome c oxidases are multi-subunit enzymes containing from 13 subunits in the mammalian mitochondrial form to 3-4 subunits in the bacterial forms.Link to AmiGO
0.0412GO:0009553The process whose specific outcome is the progression of the embryo sac over time, from its formation to the mature structure. The process begins with the meiosis of the megasporocyte to form four haploid megaspores. Three of the megaspores disintegrate, and the fourth undergoes mitosis giving rise to a binucleate syncytial embryo sac. The two haploid nuclei migrate to the opposite poles of the embryo sac and then undergo two rounds of mitosis generating four haploid nuclei at each pole. One nucleus from each set of four migrates to the center of the cell. Cellularization occurs, resulting in an eight-nucleate seven-celled structure. This structure contains two synergid cells and an egg cell at the micropylar end, and three antipodal cells at the other end. A binucleate endosperm mother cell is formed at the center. The two polar nuclei fuse resulting in a mononucleate diploid endosperm mother cell. The three antipodal cells degenerate.Link to AmiGO
0.0403GO:0048366The process whose specific outcome is the progression of the leaf over time, from its formation to the mature structure.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.055303018RNA degradationLink to KEGG PATHWAY
0.050303050ProteasomeLink to KEGG PATHWAY
0.043200510N-Glycan biosynthesisLink 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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