Co-expression analysis

Gene ID At5g54200
Gene name WD-40 repeat family protein
Module size 56 genes
NF 0.20
%ile 17.9



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
1.00100.01.00At5g54200835508WD-40 repeat family proteinF:signal transducer activity;P:signal transduction;C:heterotrimeric G-protein complex;MFBOPAVO.I.H.G.S.X.
0.4558.30.86At2g24230816957leucine-rich repeat transmembrane protein kinase, putativeF:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.H.G.S.X.
0.4253.90.86At3g53240824491AtRLP45 (Receptor Like Protein 45)F:protein binding;P:signal transduction;C:unknown;PMOBFAVO.I.H.G.S.X.
0.4050.80.87At5g41060834108zinc finger (DHHC type) family proteinF:zinc ion binding;P:unknown;C:plasma membrane;MOFPO.I.H.G.S.X.
0.3643.60.87At1g68060843134ATMAP70-1 (microtubule-associated proteins 70-1)Encodes a microtubule associated protein (MAP70-1). Expressed in all tissues.O.I.H.G.S.X.
0.3439.80.87At2g20300816549ALE2 (Abnormal Leaf Shape 2)Encodes ABNORMAL LEAF SHAPE 2 (ALE2), a receptor-like protein kinase (RLK) with a cluster of basic amino acid residues followed by a cysteine-containing sequence in the putative extracellular domain. Function together with ACR4 (Arabidopsis homolog of the Crinkly4) and ALE1 in positively regulating protoderm-specific gene expression and for the formation of leafy organs. ale2 mutants have various epidermal defects, including disorganization of epidermis-related tissues, defects in the leaf cuticle and the fusion of organs.O.I.H.G.S.X.
0.3439.80.88At4g23440828443nucleoside-triphosphatase/ nucleotide binding / transmembrane receptorF:transmembrane receptor activity, nucleoside-triphosphatase activity, nucleotide binding;P:signal transduction, innate immune response;C:plasma membrane;BPFOMAO.I.H.G.S.X.
0.3439.80.87At5g10020830865leucine-rich repeat transmembrane protein kinase, putativeF:protein binding, protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:cytosol, plasma membrane;PMOBFVAO.I.H.G.S.X.
0.3338.10.87At5g23430832409transducin 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.
0.3133.80.87At4g14920827150DNA binding / protein binding / zinc ion bindingF:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:nucleus;MPFOO.I.H.G.S.X.
0.3133.80.89At1g19870838575iqd32 (IQ-domain 32)F:calmodulin binding;P:biological_process unknown;C:cytosol, nucleus, plasma membrane, chloroplast envelope;MOFBPVAO.I.H.G.S.X.
0.2624.40.87At3g50780824242-F:unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.2522.60.87At1g13170837875ORP1D (OSBP(OXYSTEROL BINDING PROTEIN)-RELATED PROTEIN 1D)F:oxysterol binding;P:steroid metabolic process;C:unknown;MFOPO.I.H.G.S.X.
0.2522.60.86At2g17020816205F-box family protein (FBL10)F:ubiquitin-protein ligase activity, protein binding;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;MPBFOVO.I.H.G.S.X.
0.2522.60.87At3g08680820015leucine-rich repeat transmembrane protein kinase, putativeF:protein serine/threonine kinase activity, kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:plasma membrane, plant-type cell wall;PMOBFVAO.I.H.G.S.X.
0.2522.60.86At1g74800843819galactosyltransferase family proteinF:transferase activity, transferring hexosyl groups, transferase activity, transferring glycosyl groups;P:protein amino acid glycosylation;C:membrane;MPOFBO.I.H.G.S.X.
0.2522.60.87At5g40740834074unknown proteinF:unknown;P:biological_process unknown;C:unknown;OBFMPO.I.H.G.S.X.
0.2319.30.88At2g20680816596glycosyl hydrolase family 5 protein / cellulase family proteinF:cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:endomembrane system;PBFMOAO.I.H.G.S.X.
0.2217.50.86At1g64960842804bindingF:binding;P:unknown;C:mitochondrion;MOPO.I.H.G.S.X.
0.2217.50.87At3g60740825245TTN1 (TITAN 1)Encodes tubulin-folding cofactor D. Mutants arrest during embryogenesis with embryos that are small, mushroom-shaped ('pilz') and consist of only one or few large cells each containing one or more variably enlarged nuclei and often cell wall stubs. Gene product necessary for continuous microtubule organization.O.I.H.G.S.X.
0.2217.50.86At1g21700838774ATSWI3C (SWITCH/SUCROSE NONFERMENTING 3C)a member of the Arabidopsis SWI3 gene family. Protein physically interacts with ATSWI3B and ATSWI3A, the other two members of the SWI3 family. Homologous to yeast SWI3 & RSC8, components of the SWI/SNF and RSC chromatin remodeling complexes. Referred to as CHB3 in Zhou et al (2003).O.I.H.G.S.X.
0.2115.80.89At4g12640826877RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MFPOBAO.I.H.G.S.X.
0.2115.80.86At1g79990844339protein binding / structural moleculeF:protein binding, structural molecule activity;P:intracellular protein transport, vesicle-mediated transport;C:membrane coat, endomembrane system, COPI vesicle coat;MFOBPAVO.I.H.G.S.X.
0.2014.40.87At3g23900821973RNA recognition motif (RRM)-containing proteinF:nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.2014.40.86At4g11450826749unknown proteinF:unknown;P:biological_process unknown;C:chloroplast;PMOO.I.H.G.S.X.
0.1912.70.87At4g16650827366unknown proteinF:molecular_function unknown;P:biological_process unknown;C:Golgi apparatus;PO.I.H.G.S.X.
0.1912.70.86At4g32730829409PC-MYB1Encodes a putative c-myb-like transcription factor with three MYB repeats.O.I.H.G.S.X.
0.1912.70.86At5g38880833879unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAO.I.H.G.S.X.
0.1811.40.86At1g74690843808IQD31 (IQ-domain 31)F:calmodulin binding;P:biological_process unknown;C:cytosol, plasma membrane;MOFPBVAO.I.H.G.S.X.
0.1811.40.86At1g21480838746exostosin family proteinF:catalytic activity;P:biological_process unknown;C:Golgi apparatus, membrane;PMOBFO.I.H.G.S.X.
0.1811.40.86At3g09670820124PWWP domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFBO.I.H.G.S.X.
0.1811.40.87At1g53050841739protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;MPOFBVAO.I.H.G.S.X.
0.1710.20.86At5g06050830492dehydration-responsive protein-relatedF:unknown;P:biological_process unknown;C:endomembrane system;PBOMO.I.H.G.S.X.
0.1710.20.86At5g03415831847DPBEncodes a homolog of the animal DP protein. DP, in animals, forms a heterodimer with E2F and plays a central role in G1/S transition in the cell division cycle. DPB has been shown to interact with non phosphorylated E2Fc; when E2Fc is phosphorylated, the formation of the E2Fc/DPB heterodimer is lost.O.I.H.G.S.X.
0.1710.20.87At1g55130841956endomembrane protein 70, putativeF:unknown;P:unknown;C:integral to membrane, Golgi apparatus;MPOFBO.I.H.G.S.X.
0.1710.20.86At2g19950816514GC1 (Golgin Candidate 1)This gene is predicted to encode a protein that functions as a Golgi apparatus structural component known as a golgin in mammals and yeast. A fluorescently-tagged version of GC1 co-localizes with Golgi markers, and this localization appears to be replicated using the C-terminal (558-715 aa) portion of the protein.O.I.H.G.S.X.
0.1710.20.86At3g17450821009hAT dimerisation domain-containing proteinF:protein dimerization activity, DNA binding;P:biological_process unknown;C:cellular_component unknown;POMVFBO.I.H.G.S.X.
0.1710.20.87At1g01510839401AN (ANGUSTIFOLIA)Encodes a homolog of human CtBP. Mutant has longer and thicker leaves than wild type. Involved in controlling polar cell expansion in the leaf width direction.O.I.H.G.S.X.
0.1710.20.86At1g20670838655DNA-binding bromodomain-containing proteinF:DNA binding;P:biological_process unknown;C:cellular_component unknown;OMFPBVO.I.H.G.S.X.
0.1710.20.86At3g58580825027hydrolaseF:hydrolase activity;P:unknown;C:cellular_component unknown;MFOPBO.I.H.G.S.X.
0.168.80.86At5g47820834833FRA1 (FRAGILE FIBER 1)encodes a kinesin-like protein with an N-terminal microtubule binding motor domain. Protein is localized to the periphery of the cytoplasm and mutants in the gene exhibit altered orientation of cellulose microfibrils and reduced mechanical strength of fibers.O.I.H.G.S.X.
0.168.80.86At5g48520834908unknown proteinF:molecular_function unknown;P:biological_process unknown;C:nucleus;MOPFBO.I.H.G.S.X.
0.168.80.87At2g35110818077GRL (GNARLED)Component of the WAVE protein complex which act as activators of ARP2/3 complex involved in actin nucleation. Required for trichome morphogenesis. Mutant displays distorted trichomes, a phenotype that can be phenocopied by treatment of WT plants with actin-interacting drugs.O.I.H.G.S.X.
0.157.80.87At4g09630826549-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBVAO.I.H.G.S.X.
0.157.80.87At3g13222820513GIP1 (GBF-INTERACTING PROTEIN 1)Encodes a protein that binds to G-box binding transcription factors and enhances their binding affinities to G-box in vitro. This protein localizes to the nucleus and is expressed predominantly in the root.O.I.H.G.S.X.
0.157.80.87At2g30800817631HVT1 (HELICASE IN VASCULAR TISSUE AND TAPETUM)Has RNA or DNA helicase activity and expressed specifically in tapetum and vascular tissue. First identified member of a new group of the mle helicase group of the DEAH family.O.I.H.G.S.X.
0.146.80.86At2g25180817056ARR12 (ARABIDOPSIS RESPONSE REGULATOR 12)Encodes an Arabidopsis response regulator (ARR) protein that acts in concert with other type-B ARRs in the cytokinin signaling pathway.O.I.H.G.S.X.
0.135.80.86At2g44150819021ASHH3 (HISTONE-LYSINE N-METHYLTRANSFERASE ASHH3)F:histone-lysine N-methyltransferase activity;P:biological_process unknown;C:nucleus;MOPFBAO.I.H.G.S.X.
0.135.80.86At2g40980818698-F:unknown;P:unknown;C:plasma membrane;BPOO.I.H.G.S.X.
0.135.80.87At3g17900821058unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMFOO.I.H.G.S.X.
0.124.90.86At4g38200829976guanine nucleotide exchange family proteinF:binding, ARF guanyl-nucleotide exchange factor activity, guanyl-nucleotide exchange factor activity;P:regulation of ARF protein signal transduction;C:chloroplast;MFOPBO.I.H.G.S.X.
0.114.10.87At5g165053770617transposable element geneF:unknown;P:unknown;C:unknownO.I.H.G.S.X.
0.114.10.87At5g04420830321kelch repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus;MOPFBVAO.I.H.G.S.X.
0.114.10.86At2g05230815071DNAJ heat shock N-terminal domain-containing proteinF:heat shock protein binding;P:protein folding;C:cellular_component unknown;BOMPFAVO.I.H.G.S.X.
0.082.30.86At5g14790831331bindingF:binding;P:biological_process unknown;C:cellular_component unknown;MPOFO.I.H.G.S.X.
0.071.90.86At5g61840836306GUT1F:glucuronoxylan glucuronosyltransferase activity, catalytic activity;P:secondary cell wall biogenesis, glucuronoxylan biosynthetic process;C:Golgi apparatus, membrane;PMOBFO.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
54.899.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.499.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.299.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
48.299.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
48.299.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.499.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.599.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.899.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.599.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.999.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.999.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
38.899.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.499.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.399.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.199.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
37.899.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.399.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.199.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.099.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.499.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.199.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.699.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.599.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.599.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.299.7GSM184905Arabidopsis, root cells, protophloem, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
24.299.6GSM184906Arabidopsis, root cells, protophloem, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
23.799.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
17.699.5GSM184904Arabidopsis, root cells, protophloem, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
15.299.4GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
14.399.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
13.499.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.099.4GSM258002LMPC-derived phloem_1GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO
11.699.3GSM67086Arabidopsis_Stigma02GSE3056Arabidopsis Pollination StudyLink to GEO
11.499.3GSM258003LMPC-derived phloem_2GSE10247Transcriptome analysis of the Arabidopsis phloemLink to GEO
10.199.2GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.199.2E-ATMX-35-raw-cel-1574334832
10.099.2GSM184917Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.899.1E-ATMX-35-raw-cel-1574334816
9.699.1GSM216973Vector_shoots_4h_GA4+DEX_repl1GSE8741DELLA protein direct targets in ArabidopsisLink to GEO
9.299.1GSM216981Vector_shoots_4h_GA4+DEX_repl2GSE8741DELLA protein direct targets in ArabidopsisLink to GEO
8.899.0GSM67087Arabidopsis_Stigma03GSE3056Arabidopsis Pollination StudyLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0351GO:0010068The formation of the primary meristem or meristematic tissue that gives rise to the epidermis.Link to AmiGO
0.0351GO:0043388Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process by which a gene product interacts selectively with DNA (deoxyribonucleic acid).Link to AmiGO
0.0352GO:0048367The process whose specific outcome is the progression of the shoot 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

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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