Co-expression analysis

Gene ID At3g50530
Gene name CRK (CDPK-related kinase)
Module size 61 genes
NF 0.26
%ile 29.7



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
1.00100.01.00At3g50530824217CRK (CDPK-related kinase)CDPK-related kinaseO.I.H.G.S.X.
0.4963.50.89At1g63690842673protease-associated (PA) domain-containing proteinF:peptidase activity, aspartic-type endopeptidase activity;P:proteolysis;C:plasma membrane;MPOBFO.I.H.G.S.X.
0.4862.50.88At1g22060838811-F:unknown;P:unknown;C:vacuole;MOBFPAVO.I.H.G.S.X.
0.4355.30.88At5g47820834833FRA1 (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.
0.4253.90.89At1g28440839742HSL1 (HAESA-Like 1)F:protein serine/threonine kinase activity, kinase activity, ATP binding;P:transmembrane receptor protein tyrosine kinase signaling pathway, protein amino acid phosphorylation;C:unknown;MPOBFVAO.I.H.G.S.X.
0.4152.40.88At5g08390830737-F:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOPBAVO.I.H.G.S.X.
0.3846.70.89At2g38440818425SCAR2 (SCAR HOMOLOG 2)Encodes a subunit of the WAVE complex. The WAVE complex is required for activation of ARP2/3 complex which functions in actin microfilament nucleation and branching. Mutations cause defects in both the actin and microtubule cytoskeletons that result in aberrant epidermal cell expansion. itb1 mutants showed irregularities in trichome branch positioning and expansion. The SHD domain of this protein binds to BRK1 and overexpression of the SHD domain results in a dominant negative phenotype.O.I.H.G.S.X.
0.3846.70.88At1g10870837629AGD4 (ARF-GAP domain 4)A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes. AGD4 belongs to the Class 1, together with AGD1, AGD2, and AGD3.O.I.H.G.S.X.
0.3541.60.88At5g27970832867bindingF:binding;P:biological_process unknown;C:cellular_component unknown;MFOPBO.I.H.G.S.X.
0.3439.80.88At2g32950817857COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1)Represses photomorphogenesis and induces skotomorphogenesis in the dark. Contains a ring finger zinc-binding motif, a coiled-coil domain, and several WD-40 repeats, similar to G-beta proteins. The C-terminus has homology to TAFII80, a subunit of the TFIID component of the RNA polymerase II of Drosophila. Nuclear localization in the dark and cytoplasmic in the light.O.I.H.G.S.X.
0.3338.10.90At1g54610841903protein kinase family proteinF:protein serine/threonine kinase activity, protein tyrosine 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.
0.3338.10.89At4g16650827366unknown proteinF:molecular_function unknown;P:biological_process unknown;C:Golgi apparatus;PO.I.H.G.S.X.
0.3338.10.88At5g47780834829GAUT4 (Galacturonosyltransferase 4)Encodes a protein with putative galacturonosyltransferase activity.O.I.H.G.S.X.
0.3338.10.88At3g12010820375-F:molecular_function unknown;P:biological_process unknown;C:unknown;MOPO.I.H.G.S.X.
0.3235.70.89At1g53050841739protein 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.
0.3235.70.89At3g51310824294VPS35C (VPS35 HOMOLOG C)Homolog of yeast retromer subunit VPS35. Part of a retromer-like protein complex involved in endosome to lysosome protein transport.O.I.H.G.S.X.
0.3235.70.88At3g06650819845ACLB-1One of the two genes encoding subunit B of the trimeric enzyme ATP Citrate lyaseO.I.H.G.S.X.
0.3235.70.89At1g12820837838AFB3 (AUXIN SIGNALING F-BOX 3)F:auxin binding, ubiquitin-protein ligase activity;P:stamen development, pollen maturation, response to molecule of bacterial origin;C:cellular_component unknown;PMFOBO.I.H.G.S.X.
0.3133.80.88At2g46560819268transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:unknown;C:CUL4 RING ubiquitin ligase complex;BFMOPO.I.H.G.S.X.
0.3133.80.89At1g60220842317ULP1D (UB-LIKE PROTEASE 1D)Encodes a deSUMOylating enzyme. In vitro it has both peptidase activity and isopeptidase activity: it can cleave C-terminal residues from SUMO to activate it for attachment to a target protein and it can also act on the isopeptide bond between SUMO and another protein. sGFP:OTS1 protein accumulates in the nucleus. Double mutant analysis with ULP1C/OTS2 indicates that these genes are involved in salt stress responses and flowering time regulation. Over-expression of 35S:OTS1 increases salt tolerance and reduces the level of SUMO-conjugated proteins. OTS1 transcript levels do not appear to change in response to salt, but, salt stress reduces the level of OTS1 protein in a proteasome-dependent manner.O.I.H.G.S.X.
0.3133.80.88At1g58230842191WD-40 repeat family protein / beige-relatedF:unknown;P:signal transduction;C:mitochondrion;MBOFPAO.I.H.G.S.X.
0.3133.80.89At4g02680828205EOL1 (ETO1-LIKE 1)Encodes a paralog of ETO1, which is a negative regulator of ACS5 (a key enzyme in ethylene biosynthesis pathway). EOL1 also interacts with and inhibits the activity of ACS5.O.I.H.G.S.X.
0.3032.10.89At5g35180833472phosphoinositide bindingF:phosphoinositide binding;P:signal transduction;C:plasma membrane;POMFVO.I.H.G.S.X.
0.2930.30.88At5g22760832339PHD finger family proteinF:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:unknown;MPFOO.I.H.G.S.X.
0.2930.30.88At5g50000835064protein kinase, putativeF:protein serine/threonine/tyrosine kinase activity, kinase activity;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVAO.I.H.G.S.X.
0.2930.30.88At3g15410820780leucine-rich repeat family proteinF:protein binding;P:signal transduction;C:unknown;MPBOFAVO.I.H.G.S.X.
0.2930.30.88At2g36720818244PHD finger transcription factor, putativeF:protein binding, DNA binding, zinc ion binding;P:regulation of transcription, DNA-dependent;C:nucleus;MPFOO.I.H.G.S.X.
0.2930.30.88At3g55480824714adaptin family proteinF:protein binding, binding;P:intracellular protein transport, vesicle-mediated transport;C:membrane coat, endomembrane system;BMFOPO.I.H.G.S.X.
0.2830.30.88At3g50780824242-F:unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.2726.20.88At4g38520830009protein phosphatase 2C family protein / PP2C family proteinF:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:protein serine/threonine phosphatase complex;MPOFBVO.I.H.G.S.X.
0.2726.20.89At3g17750821043protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cytosol, plasma membrane;MOPFBVAO.I.H.G.S.X.
0.2624.40.89At2g20190816539CLASP (CLIP-ASSOCIATED PROTEIN)Encodes a microtubule-associated protein that is involved in both cell division and cell expansion. It likely promotes microtubule stability.O.I.H.G.S.X.
0.2624.40.88At5g28850833004calcium-binding EF hand family proteinF:calcium ion binding;P:biological_process unknown;C:endomembrane system;MOPFO.I.H.G.S.X.
0.2624.40.88At1g60070842301binding / clathrin binding / protein binding / protein transporterF:protein transporter activity, protein binding, clathrin binding, binding;P:intracellular protein transport, vesicle-mediated transport, protein transport;C:membrane coat, Golgi apparatus part, Golgi apparatus, clathrin adaptor complex;MFOPBO.I.H.G.S.X.
0.2522.60.88At2g26770817218plectin-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOBFPAVO.I.H.G.S.X.
0.2522.60.88At5g06120830499Ran-binding protein, putativeF:protein transporter activity, binding;P:intracellular protein transport, protein import into nucleus, docking;C:nucleus, nuclear pore, cytoplasm;MOPO.I.H.G.S.X.
0.2522.60.88At3g47000823853glycosyl hydrolase family 3 proteinF:hydrolase activity, hydrolyzing O-glycosyl compounds;P:carbohydrate metabolic process;C:cellular_component unknown;BOFPAMO.I.H.G.S.X.
0.2522.60.88At3g54190824586-F:molecular_function unknown;P:biological_process unknown;C:unknown;POO.I.H.G.S.X.
0.2420.70.88At2g47900819402AtTLP3 (TUBBY LIKE PROTEIN 3)Member of TLP familyO.I.H.G.S.X.
0.2420.70.88At4g38200829976guanine 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.
0.2420.70.88At1g19430838527dehydration-responsive protein-relatedF:unknown;P:biological_process unknown;C:Golgi apparatus;MOFPBVAO.I.H.G.S.X.
0.2319.30.88At5g49650835027xylulose kinase, putativeF:xylulokinase activity, phosphotransferase activity, alcohol group as acceptor;P:carbohydrate metabolic process, xylulose catabolic process;C:cellular_component unknown;BOMFPAO.I.H.G.S.X.
0.2319.30.88At3g06580819837GALKEncodes a protein with galactose kinase activity. The gene was shown to complement the yeast Δgal1 mutant defective in the galactokinase gene GAL1.O.I.H.G.S.X.
0.2319.30.88At3g15120820743AAA-type ATPase family proteinF:nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;P:unknown;C:unknown;MOBFPAVO.I.H.G.S.X.
0.2319.30.88At1g02080839244transcriptional regulator-relatedF:transcription regulator activity;P:unknown;C:membrane;MOFBPO.I.H.G.S.X.
0.2319.30.88At2g23460816878XLG1 (EXTRA-LARGE G-PROTEIN 1)encodes a novel G-alpha protein that shares similarity to plant, yeast, and animal G-alpha proteins at the C-terminus. It contains an N-terminus that is as large as the C-terminus, is a member of a small family, and is expressed in all tissues examined, including roots, leaves, stems, flowers, and fruits.O.I.H.G.S.X.
0.2217.50.88At5g27710832833unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.2115.80.89At5g48640834921cyclin family proteinF:cyclin-dependent protein kinase activity;P:regulation of cell cycle;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.2014.40.88At1g55130841956endomembrane protein 70, putativeF:unknown;P:unknown;C:integral to membrane, Golgi apparatus;MPOFBO.I.H.G.S.X.
0.1912.70.88At3g26370822241unknown proteinF:unknown;P:unknown;C:Golgi apparatus;PO.I.H.G.S.X.
0.1912.70.88At2g22670816798IAA8IAA8 (IAA8) gene is auxin inducible.O.I.H.G.S.X.
0.1912.70.88At3g13290820529VCR (VARICOSE-RELATED)F:nucleotide binding;P:unknown;C:cellular_component unknown;MBOFPAO.I.H.G.S.X.
0.1811.40.88At3g50590824223nucleotide bindingF:nucleotide binding;P:biological_process unknown;C:plasma membrane;MBFOPVO.I.H.G.S.X.
0.1811.40.88At4g18060827531clathrin bindingF:clathrin binding;P:unknown;C:unknown;MOFPBO.I.H.G.S.X.
0.1811.40.88At5g66950836829catalytic/ pyridoxal phosphate bindingF:pyridoxal phosphate binding, catalytic activity;P:biological_process unknown;C:plasma membrane;PMFOBAO.I.H.G.S.X.
0.1710.20.87At5g18190831937protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MBOPFVAO.I.H.G.S.X.
0.168.80.88At5g63840836504RSW3 (RADIAL SWELLING 3)radial swelling mutant shown to be specifically impaired in cellulose production. Encodes the alpha-subunit of a glucosidase II enzyme.O.I.H.G.S.X.
0.157.80.88At1g14570838019UBX domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOBO.I.H.G.S.X.
0.157.80.88At1g25420839128unknown proteinF:unknown;P:biological_process unknown;C:unknown;PMFOO.I.H.G.S.X.
0.146.80.88At3g60030825173SPL12 (squamosa promoter-binding protein-like 12)F:transcription factor activity;P:regulation of transcription;C:nucleus;PMOO.I.H.G.S.X.
0.103.40.88At4g16360827331AMP-activated protein kinaseF:AMP-activated protein kinase activity;P:N-terminal protein myristoylation;C:chloroplast;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
95.699.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
89.199.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
62.099.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
60.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
59.899.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.399.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
53.699.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
52.399.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.399.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.699.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.699.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.999.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.899.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.499.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.699.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.499.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.399.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
42.799.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.399.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.499.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.199.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.399.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.799.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.399.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
27.699.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.199.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.699.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
19.699.6GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
16.199.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.199.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.699.0GSM270814Arabidopsis cell culture, 4 h_control_rep1GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
8.699.0GSM134301Penfield_1-3_endosperm-control_Rep3_ATH1GSE5751The early post-germinative embryo and endosperm transcriptomes in ArabidopsisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0364GO:0006886The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.Link to AmiGO
0.0321GO:0005997The chemical reactions and pathways involving xylulose, the ketopentose threo-2-pentulose.Link to AmiGO
0.0321GO:0016337The attachment of one cell to another cell via adhesion molecules.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.043200052Galactose metabolismLink to KEGG PATHWAY
0.028200500Starch and sucrose metabolismLink to KEGG PATHWAY
0.024100460Cyanoamino acid metabolismLink 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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