Co-expression analysis

Gene ID At5g37490
Gene name U-box domain-containing protein
Module size 40 genes
NF 0.44
%ile 62.1



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
0.6781.61.00At5g37490833727U-box domain-containing proteinF:ubiquitin-protein ligase activity, binding;P:response to chitin;C:ubiquitin ligase complex;PMOFBVO.I.H.G.S.X.
0.6882.20.71At4g14455827091ATBET12Encodes a Bet1/Sft1-like SNARE protein, which can only partially suppresses the temperature-sensitive growth defect in sft1-1 yeast cells; however, it cannot support the deletion of the yeast BET1 gene (bet1Δ). In yeast, Bet1p is the v-SNARE (soluble N-ethylmaleimide-sensitive factor adaptor protein receptor, V-type) involved in trafficking between the ER and Golgi.O.I.H.G.S.X.
0.6075.70.71At2g40740818669WRKY55member of WRKY Transcription Factor; Group IIIO.I.H.G.S.X.
0.5974.70.69At1g07160837227protein phosphatase 2C, putative / PP2C, putativeF:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:chloroplast, protein serine/threonine phosphatase complex;MPOFBVAO.I.H.G.S.X.
0.5773.80.69At5g47850834836CCR4 (ARABIDOPSIS THALIANA CRINKLY4 RELATED 4)F:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.H.G.S.X.
0.5673.00.71At5g27420832801zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:response to chitin, response to abscisic acid stimulus;C:endomembrane system;PMOFVO.I.H.G.S.X.
0.5570.60.67At2g23270816859unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.5570.60.70At5g05300830412unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.5368.60.73At1g72950843626disease resistance protein (TIR-NBS class), putativeF:transmembrane receptor activity;P:signal transduction, defense response, innate immune response;C:intrinsic to membrane;PBMO.I.H.G.S.X.
0.5166.30.68At1g16090838179WAKL7 (wall associated kinase-like 7)WAK-like kinaseO.I.H.G.S.X.
0.5166.30.69At4g28460828963unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.5166.30.64At5g24110832476WRKY30member of WRKY Transcription Factor; Group IIIO.I.H.G.S.X.
0.4963.50.66At2g32030817763GCN5-related N-acetyltransferase (GNAT) family proteinF:N-acetyltransferase activity;P:metabolic process;C:cellular_component unknown;BOFPAVMO.I.H.G.S.X.
0.4862.50.64At2g37430818319zinc finger (C2H2 type) family protein (ZAT11)F:transcription factor activity, zinc ion binding, nucleic acid binding;P:response to chitin, regulation of transcription;C:intracellular;MPOFO.I.H.G.S.X.
0.4862.50.64At2g44070819013GTP binding / translation initiation factorF:GTP binding, translation initiation factor activity;P:translational initiation, cellular metabolic process;C:eukaryotic translation initiation factor 2B complex;OBMFAPO.I.H.G.S.X.
0.4862.50.65At1g72520843584lipoxygenase, putativeF:electron carrier activity, oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen, lipoxygenase activity, iron ion binding, metal ion binding;P:growth, jasmonic acid biosynthetic process, response to wounding, defense response;C:chloroplast;PMBFOO.I.H.G.S.X.
0.4862.50.68At5g67450836881AZF1 (ARABIDOPSIS ZINC-FINGER PROTEIN 1)Encodes zinc-finger protein. mRNA levels are elevated in response to low temperature, cold temperatures and high salt. The protein is localized to the nucleus and acts as a transcriptional repressor.O.I.H.G.S.X.
0.4862.50.67At2g21910816727CYP96A5member of CYP96AO.I.H.G.S.X.
0.4862.50.68At2g27310817274F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.4761.20.66At4g16820827388lipase class 3 family proteinF:triacylglycerol lipase activity;P:lipid metabolic process;C:unknown;POFBMVO.I.H.G.S.X.
0.4659.80.65At2g25735817115unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.4659.80.64At3g23230821901ethylene-responsive factor, putativeencodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5.O.I.H.G.S.X.
0.4457.20.67At1g58420842211-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.4457.20.64At5g66620836794DAR6 (DA1-RELATED PROTEIN 6)F:zinc ion binding;P:unknown;C:unknown;MOBFPVAO.I.H.G.S.X.
0.4253.90.68At5g14700831322cinnamoyl-CoA reductase-relatedF:binding, 3-beta-hydroxy-delta5-steroid dehydrogenase activity, cinnamoyl-CoA reductase activity, catalytic activity;P:lignin biosynthetic process, steroid biosynthetic process, metabolic process;C:cellular_component unknown;POBFMVAO.I.H.G.S.X.
0.4152.40.71At4g00970827936protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.H.G.S.X.
0.4050.80.64At1g35210840410unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;POO.I.H.G.S.X.
0.3948.40.65At2g27320817275unknown proteinF:unknown;P:biological_process unknown;C:endomembrane system;PFBO.I.H.G.S.X.
0.3948.40.63At4g23810828481WRKY53member of WRKY Transcription Factor; Group IIIO.I.H.G.S.X.
0.3948.40.64At2g35710818140glycogenin glucosyltransferase (glycogenin)-relatedF:transferase activity, transferring hexosyl groups, transferase activity, transferring glycosyl groups;P:carbohydrate biosynthetic process, biosynthetic process;C:endomembrane system;PMFOBVO.I.H.G.S.X.
0.3948.40.64At5g61900836311BON1 (BONZAI 1)Encodes a plasma-membrane localized, copine-like protein, which is a member of a newly identified class of calcium-dependent, phospholipid binding proteins that are present in a wide range of organisms. Mutants exhibit temperature-sensitive growth defects and increased hypersensitive response where permissive conditions are low temperature (22 degrees Celsius) and low humidity. Gene is expressed at 22 but not at 28 (restrictive condition) degrees. Lethality of double mutants with BON3 can be partially suppressed by SNC1. Double mutants show defects in development that are genetically separable from hypersensitive/cell death response.O.I.H.G.S.X.
0.3745.00.70At4g38530830010ATPLC1 (ARABIDOPSIS THALIANA PHOSPHOLIPASE C 1)Encodes a putative phosphoinositide-specific phospholipase C. There are two genes called ATPLC1, one corresponding to AT4g38530 (this one) and one corresponding to AT5g58670.O.I.H.G.S.X.
0.3643.60.67At4g23190828418CRK11 (CYSTEINE-RICH RLK11)Encodes putative receptor-like protein kinase that is induced by the soil-borne vascular bacteria, Ralstonia solanacearum. Naming convention from Chen et al 2003 (PMID 14756307)O.I.H.G.S.X.
0.3643.60.70At4g25350828638SHB1 (SHORT HYPOCOTYL UNDER BLUE1)SHB1 encodes a nuclear and cytosolic protein that has motifs homologous with SYG1 protein family members. Acts in cryptochrome signaling. Overexpression of SHB1 enhanced the expression of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) under red light and promoted proteasome-mediated degradation of phytochrome A and hypocotyl elongation under far-red light. A knockout allele suppressed LONG HYPOCOTYL IN FAR-RED LIGHT1 (HFR1) expression and showed several deetiolation phenotypes. Acts upstream of HFR1. Regulates seed development.O.I.H.G.S.X.
0.3541.60.64At3g08720820019S6K2 (ARABIDOPSIS THALIANA SERINE/THREONINE PROTEIN KINASE 2)Encodes a ribosomal-protein S6 kinase. Gene expression is induced by cold and salt (NaCl). Activation of AtS6k is regulated by 1-naphthylacetic acid and kinetin, at least in part, via a lipid kinase-dependent pathway. Phosphorylates specifically mammalian and plant S6 at 25 degrees C but not at 37 degrees C. Involved in translational up-regulation of ribosomal proteins.O.I.H.G.S.X.
0.3439.80.66At5g47230834770ERF5 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 5)encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-5). The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5.O.I.H.G.S.X.
0.3338.10.65At1g24140839026matrixin family proteinF:metallopeptidase activity, metalloendopeptidase activity;P:proteolysis, metabolic process;C:anchored to membrane;MOPBVAFO.I.H.G.S.X.
0.3235.70.67At5g41740834177disease resistance protein (TIR-NBS-LRR class), putativeF:transmembrane receptor activity, protein binding, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:signal transduction, defense response, apoptosis, innate immune response;C:intrinsic to membrane, chloroplast;PMBOFAO.I.H.G.S.X.
0.2930.30.64At1g686903767664ATP binding / protein kinase/ protein serine/threonine kinaseF:protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplastO.I.H.G.S.X.
0.2624.40.65At2g050503767735catalyticF:catalytic activity;P:biological_process unknown;C:cellular_component unknownO.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
121.499.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
116.599.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
90.199.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
86.699.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
69.799.9GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
61.499.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
61.099.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
54.799.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
54.799.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
52.899.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
52.199.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.699.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.299.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
49.099.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.299.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.199.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.599.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
46.399.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.599.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.399.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.999.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.999.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.999.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.999.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
38.699.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.599.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.099.7GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
20.899.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
18.599.5GSM284386Arabidopsis GSUS3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
16.799.5GSM133776Lindsey_1-1_globular-apical_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.799.4GSM284387Arabidopsis GSUS4bGSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
13.299.4GSM311275Laser capture microdissected (LCM) micropylar endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
12.899.3GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.299.3GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
12.199.3E-MEXP-807-raw-cel-1173273252
11.999.3GSM142624MC002_ATH1_A1.2-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.399.3GSM311276Laser capture microdissected (LCM) micropylar endospermr at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
10.599.2GSM265431Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO
9.899.1GSM142641MC002_ATH1_A7.1-dubos-wLhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.599.1GSM133756Lindsey_1-10_heart-stage-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
8.899.0GSM142643MC002_ATH1_A7.3-dubos-wLhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0912GO:0045793Any process that increases cell size.Link to AmiGO
0.0847GO:0010200A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chitin stimulus.Link to AmiGO
0.0612GO:0009816A response of an organism to a bacterium that prevents the occurrence or spread of disease.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.029100592alpha-Linolenic acid metabolismLink to KEGG PATHWAY
0.023104130SNARE interactions in vesicular transportLink to KEGG PATHWAY
0.006101070Biosynthesis of plant hormonesLink 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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