Co-expression analysis

Gene ID At4g09830
Gene name -
Module size 35 genes
NF 0.27
%ile 30.9



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
1.00100.01.00At4g09830826572-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.5267.40.89At4g27130828821eukaryotic translation initiation factor SUI1, putativeF:translation initiation factor activity;P:translational initiation, translation;C:cellular_component unknown;MPFOAVBO.I.H.G.S.X.
0.4862.50.93At3g55770824743LIM domain-containing proteinF:zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MOPFO.I.H.G.S.X.
0.4355.30.89At2g36900818264MEMB11 (MEMBRIN 11)member of Membrin Gene FamilyO.I.H.G.S.X.
0.3846.70.92At5g20520832174WAV2 (WAVY GROWTH 2)Encodes a Bem46-like protein. WAV2 negatively regulates root bending when roots alter their growth direction. It's not involved in sensing environmental stimuli (e.g. gravity, light, water, touch).O.I.H.G.S.X.
0.3745.00.89At3g01520821122universal stress protein (USP) family proteinF:molecular_function unknown;P:N-terminal protein myristoylation, response to stress;C:plasma membrane;BPAMOFO.I.H.G.S.X.
0.3541.60.91At1g17530838327ATTIM23-1 (TRANSLOCASE OF INNER MITOCHONDRIAL MEMBRANE 23)Encodes a translocase of inner mitochondrial membrane.O.I.H.G.S.X.
0.3541.60.90At1g15400838110unknown proteinF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;POBO.I.H.G.S.X.
0.3439.80.91At1g51200841543zinc finger (AN1-like) family proteinF:DNA binding, zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MPOVFO.I.H.G.S.X.
0.3032.10.89At5g14240831274-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBO.I.H.G.S.X.
0.2930.30.90At5g18110831929NCBP (NOVEL CAP-BINDING PROTEIN)F:RNA binding, translation initiation factor activity;P:translational initiation;C:cytoplasm;MOFPO.I.H.G.S.X.
0.2930.30.90At5g10860830953CBS domain-containing proteinF:unknown;P:response to salt stress;C:mitochondrion;BOAPFMO.I.H.G.S.X.
0.2726.20.89At1g43700840957VIP1 (VIRE2-INTERACTING PROTEIN 1)Encodes a VirE2-interacting protein. VIP1 mediates nuclear translocation of VirE2 via its amino half, and interacts with histone H2A via it carboxyl half.O.I.H.G.S.X.
0.2624.40.91At2g21240816663BPC4 (BASIC PENTACYSTEINE 4)F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMBO.I.H.G.S.X.
0.2522.60.90At3g62290825402ATARFA1E (ADP-ribosylation factor A1E)A member of ARF GTPase family. A thaliana has 21 members of this family, known to be essential for vesicle coating and uncoating and functions in GTP-binding. The gene is shown to play a role in cell division, cell expansion and cellulose production using antisense construct.O.I.H.G.S.X.
0.2522.60.90At5g67380836873CKA1 (CASEIN KINASE ALPHA 1)casein kinase II catalytic subunit alphaO.I.H.G.S.X.
0.2522.60.89At1g36980840608unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.2522.60.89At3g25910822188zinc ion bindingF:zinc ion binding;P:biological_process unknown;C:intracellular;MPOFBVO.I.H.G.S.X.
0.2522.60.90At5g35330833487MBD02 (METHYL-CPG-BINDING DOMAIN PROTEIN 02)Protein containing methyl-CpG-binding domain.Has sequence similarity to human MBD proteins.O.I.H.G.S.X.
0.2420.70.90At1g56280842081ATDI19Encodes a gene whose transcript level in root and leaves increases to progressive drought stress. The increase in transcript level is independent from abscisic acid level. Sequence is not similar to any protein of known function. It appears to be a member of plant-specific gene family. It's phosphorylated by AtCPK11 in a Ca(2+)-dependent manner at Thr105 and Ser107 within the AtDi19 bipartite nuclear localization signalO.I.H.G.S.X.
0.2420.70.91At3g60600825231VAP (VESICLE ASSOCIATED PROTEIN)Encodes VAP27 (for Vesicle-Associated Protein). VAP27 has high homology to the VAP33 family of SNARE-like proteins from animals. May be involved in vesicular transport to or from the ER. Located exclusively in limiting membrane of protein storage vacuoles. Binds SRC2.O.I.H.G.S.X.
0.2319.30.90At4g27000828808ATRBP45CF:RNA binding;P:unknown;C:unknown;MPFOBAVO.I.H.G.S.X.
0.2319.30.89At3g18215821349unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PBOO.I.H.G.S.X.
0.2217.50.89At3g07560819945PEX13 (PEROXIN 13)Encodes peroxin 13 (PEX13) involved in protein transport into peroxisomes.O.I.H.G.S.X.
0.2217.50.90At5g16470831508zinc finger (C2H2 type) family proteinF:transcription factor activity, zinc ion binding, nucleic acid binding;P:regulation of transcription;C:intracellular;POMO.I.H.G.S.X.
0.2115.80.90At1g16240838193SYP51 (SYNTAXIN OF PLANTS 51)Encodes one of 24 Arabidopsis syntaxins. Its mRNA has been shown to be expressed.O.I.H.G.S.X.
0.2014.40.90At3g48680824029GAMMA CAL2 (GAMMA CARBONIC ANHYDRASE-LIKE 2)Encodes a mitochondrial gamma carbonic anhydrase-like protein. Component of the NADH dehydrogenase complex.O.I.H.G.S.X.
0.2014.40.89At1g06400837151ARA-2small GTP-binding protein (ara-2)O.I.H.G.S.X.
0.1912.70.89At3g52560824422UEV1D-4 (UBIQUITIN E2 VARIANT 1D-4)MMZ4/UEV1D encodes a protein that may play a role in DNA damage responses and error-free post-replicative DNA repair by participating in lysine-63-based polyubiquitination reactions. UEV1D can form diubiquitin and triubiquitin chains in combination with UBC13A/UBC35 in vitro. It can also functionally complement an mms2 mutation in budding yeast, both by increasing mms2 mutant viability in the presence of the DNA damaging agent MMS, and by reducing the rate of spontaneous DNA mutation. It can also rescue an mms2 ubc13 double mutant in yeast in combination with UBC13A. MMZ4/UEV1D transcripts are found in most plant organs, like the other three MMZ/UEV1 family members, but it is normally present at higher levels. In addition, MMZ4/UEV1D is the only family member whose transcripts are detected in pollen. However, MMZ4/UEV1D transcript levels do not appear to be stress-inducible. uev1d-1 mutants are more sensitive than wild type plants to the DNA damaging agent MMS in seed germination and pollen germination assays.O.I.H.G.S.X.
0.1912.70.90At1g52740841707HTA9 (HISTONE H2A PROTEIN 9)Encodes HTA9, a histone H2A protein.O.I.H.G.S.X.
0.1811.40.90At2g37410818317ATTIM17-2Mitochondrial inner membrane translocase. Together with AtTIM17-1, TIM17-2 has a long C-terminal extension not present in other TIMs. The extension is located in the outer membrane and so TIM17-2 links the inner and outer mitochondrial membranes. The C-terminal region is essential for protein import into mitochondria via the general import pathway but is not necessary for import via the carrier pathway.O.I.H.G.S.X.
0.1710.20.89At3g11530820326vacuolar protein sorting 55 family protein / VPS55 family proteinF:transporter activity;P:transport;C:vacuole;FMPOO.I.H.G.S.X.
0.146.80.90At1g49850841408zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVBO.I.H.G.S.X.
0.124.90.89At3g22440821815hydroxyproline-rich glycoprotein family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFOBO.I.H.G.S.X.
0.092.80.89At5g63640836484VHS domain-containing protein / GAT domain-containing proteinF:protein transporter activity;P:intracellular protein transport, intra-Golgi vesicle-mediated transport;C:Golgi stack, plasma membrane;MFPOBO.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
66.899.8GSM133760Lindsey_1-12_heart-stage-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
41.799.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
41.299.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
39.299.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.299.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
38.399.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.999.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.399.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.299.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.599.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.399.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.199.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.999.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.699.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.399.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.799.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.299.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.099.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.699.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.499.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.099.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.899.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.199.6GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.499.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.399.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.699.5E-MEXP-265-raw-cel-414618394
16.399.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.899.5GSM128676Underwood_1-29_DC3000-10e8-7h_Rep2_ATH1GSE5520Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interactionLink to GEO
15.599.5E-ATMX-35-raw-cel-1574334800
14.499.4E-ATMX-35-raw-cel-1574334832
13.499.4GSM142636MC002_ATH1_A5.2-dubos-5kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
12.599.3E-MEXP-265-raw-cel-414618291
12.599.3E-MEXP-265-raw-cel-414618491
12.299.3GSM142637MC002_ATH1_A5.3-dubos-5kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.999.3GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.499.3GSM142635MC002_ATH1_A5.1-dubos-5kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.299.2GSM142846MG001_ATH1_A27-Torres-9N1GSE6176Impact of Type III effectors on plant defense responsesLink to GEO
11.299.2GSM142845MG001_ATH1_A26-Torres-8N3GSE6176Impact of Type III effectors on plant defense responsesLink to GEO
10.999.2GSM131293AtGen_6-2321_Osmoticstress-Roots-3.0h_Rep1GSE5622AtGenExpress: Stress Treatments (Osmotic stress)Link to GEO
10.599.2GSM133957Fukuda_1-2_0B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
10.199.2GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
9.399.1GSM131317AtGen_6-3321_Saltstress-Roots-3.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
9.199.1GSM131655ATGE_27_AGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
9.099.1E-MEXP-265-raw-cel-414618796
8.999.0GSM270814Arabidopsis cell culture, 4 h_control_rep1GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
8.899.0E-ATMX-35-raw-cel-1574334816
8.899.0GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
8.899.0GSM131294AtGen_6-2322_Osmoticstress-Roots-3.0h_Rep2GSE5622AtGenExpress: Stress Treatments (Osmotic stress)Link to GEO
8.899.0E-MEXP-265-raw-cel-414618693
8.799.0GSM131305AtGen_6-2621_Osmoticstress-Roots-24.0h_Rep1GSE5622AtGenExpress: Stress Treatments (Osmotic stress)Link to GEO
8.699.0GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
8.699.0GSM131302AtGen_6-2522_Osmoticstress-Roots-12.0h_Rep2GSE5622AtGenExpress: Stress Treatments (Osmotic stress)Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0541GO:0051170The directed movement of substances into the nucleus.Link to AmiGO
0.0501GO:0006301The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication. Includes pathways that remove replication-blocking lesions in conjunction with DNA replication.Link to AmiGO
0.0481GO:0016558The import of proteins into the peroxisomal matrix. A peroxisome targeting signal (PTS) binds to a soluble receptor protein in the cytosol, and the resulting complex then binds to a receptor protein in the peroxisome membrane and is imported.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.048204130SNARE interactions in vesicular transportLink 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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