Co-expression analysis

Gene ID At2g25590
Gene name agenet domain-containing protein
Module size 52 genes
NF 0.18
%ile 15.6



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
1.00100.01.00At2g25590817098agenet domain-containing proteinF:RNA binding;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.4457.20.82At4g00040828224chalcone and stilbene synthase family proteinF:transferase activity, transferring acyl groups other than amino-acyl groups, catalytic activity, acyltransferase activity;P:phenylpropanoid biosynthetic process, biosynthetic process, metabolic process;C:unknown;PBOFO.I.H.G.S.X.
0.4355.30.84At4g18120827537AML3 (ARABIDOPSIS MEI2-LIKE 3)A member of mei2-like gene family, predominantly plant-based family of genes encoding RNA binding proteins with characteristic presence of a highly conserved RNA binding motif first described in the mei2 gene of the fission yeast S. pombe. In silico analyses reveal nine mei2 -like genes in A. thaliana. They were grouped into four distinct clades, based on overall sequence similarity and subfamily-specific sequence elements. AML3 is a member of two sister clades of mei2-like gene family, AML1 through AML5, and belongs to the clade named ALM235. Among mei2-like genes, AML3 is the transcript with highest frequency of alternative splicing. Expression was detected during early embryo development (heart and torpedo stage); no accumulation was detected in vegetative and floral apices, as revealed by in situ hybridization.O.I.H.G.S.X.
0.3439.80.87At5g25560832631zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MPOFAO.I.H.G.S.X.
0.3338.10.84At1g03080838350-F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MOBFPAVO.I.H.G.S.X.
0.3133.80.84At1g26580839198-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PFO.I.H.G.S.X.
0.3133.80.81At4g36980829852unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MOFPVBO.I.H.G.S.X.
0.3032.10.86At3g26100822208regulator of chromosome condensation (RCC1) family proteinF:Ran GTPase binding;P:biological_process unknown;C:unknown;MOBPFAVO.I.H.G.S.X.
0.2726.20.81At5g66180836750-F:unknown;P:unknown;C:cellular_component unknown;BOMAFPO.I.H.G.S.X.
0.2726.20.83At2g43680818970IQD14F:calmodulin binding;P:unknown;C:plasma membrane;MBFOPVAO.I.H.G.S.X.
0.2420.70.81At1g70620843399cyclin-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.2420.70.82At1g27150839604bindingF:binding;P:biological_process unknown;C:cellular_component unknown;BOMPAO.I.H.G.S.X.
0.2319.30.82At3g27610822383-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OPBAFO.I.H.G.S.X.
0.2217.50.83At3g27260822345GTE8Kinase like protein with similarity to yeast BDF1 and human RING3 protein, which have two bromodomains GTE8 has a single bromodomainO.I.H.G.S.X.
0.2217.50.84At3g49490824111unknown proteinF:molecular_function unknown;P:unknown;C:cellular_component unknown;OMFBPO.I.H.G.S.X.
0.2115.80.83At2g34730818038myosin heavy chain-relatedF:unknown;P:unknown;C:mitochondrion;MOBFPAVO.I.H.G.S.X.
0.2014.40.83At1g72650843597TRFL6 (TRF-LIKE 6)Arabidopsis thaliana myb family transcription factor (At1g72650)O.I.H.G.S.X.
0.1912.70.82At3g57300824897INO80 (INO80 ORTHOLOG)Encodes the Arabidopsis INO80 ortholog of the SWI/SNF ATPase family. Functions as a positive regulator of DNA homologous recombination (HR). In INO80 mutants, the HR frequency is reduced to 15% of that in the wild-type. Mutation in INO80 does not affect sensitivity to genotoxic agents and efficiency of T-DNA integration. INO80 was also shown to regulate a subset of the Arabidopsis transcriptome.O.I.H.G.S.X.
0.1811.40.82At1g60490842344ATVPS34Encodes a phosphatidylinositol 3-kinase that is expressed in most plant tissues. Defects in VPS34 affect a number of celluar processes. Loss of function mutations are not transmitted through the male gametophyte due to defects in microgametogenesis therefore it is difficult to assess the effects of loss of VPS34 function in the whole plant.O.I.H.G.S.X.
0.1811.40.83At3g49590824121-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFPBVO.I.H.G.S.X.
0.1811.40.82At1g77800844117PHD finger family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;MFOPBO.I.H.G.S.X.
0.1710.20.83At2g35920818165helicase domain-containing proteinF:helicase activity, nucleic acid binding, ATP-dependent helicase activity, ATP binding;P:biological_process unknown;C:cellular_component unknown;MBOFPVO.I.H.G.S.X.
0.1710.20.82At5g27950832864kinesin motor protein-relatedF:microtubule motor activity, ATP binding;P:microtubule-based movement;C:microtubule associated complex;MOFPBO.I.H.G.S.X.
0.1710.20.81At5g43560834376meprin and TRAF homology domain-containing protein / MATH domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFBPVAO.I.H.G.S.X.
0.1710.20.82At1g53590841794NTMC2T6.1F:unknown;P:unknown;C:plasma membrane, vacuole;MPOFBVO.I.H.G.S.X.
0.1710.20.83At5g22700832333F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO.I.H.G.S.X.
0.168.80.83At5g55600835654agenet domain-containing protein / bromo-adjacent homology (BAH) domain-containing proteinF:RNA binding, DNA binding;P:biological_process unknown;C:cellular_component unknown;POMFO.I.H.G.S.X.
0.168.80.87At1g26440839185ATUPS5 (ARABIDOPSIS THALIANA UREIDE PERMEASE 5)uptake assays in a yeast mutant indicated this splice variant is not a cellular importer for allantoin, uracil or xanthineO.I.H.G.S.X.
0.168.80.81At3g61480825321-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBO.I.H.G.S.X.
0.157.80.81At1g17680838344transcription factor-relatedF:binding;P:biological_process unknown;C:cellular_component unknown;MOBFPVAO.I.H.G.S.X.
0.157.80.83At1g27520839643glycoside hydrolase family 47 proteinF:mannosyl-oligosaccharide 1,2-alpha-mannosidase activity, alpha-mannosidase activity, calcium ion binding;P:protein amino acid N-linked glycosylation;C:endomembrane system, membrane;MFOPBO.I.H.G.S.X.
0.157.80.82At1g19485838534AT hook motif-containing proteinF:DNA binding;P:regulation of transcription, DNA-dependent;C:CUL4 RING ubiquitin ligase complex;MFPOBO.I.H.G.S.X.
0.157.80.83At3g28690822499protein kinase, putativeF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVAO.I.H.G.S.X.
0.157.80.81At4g30360829159ATCNGC17member of Cyclic nucleotide gated channel familyO.I.H.G.S.X.
0.157.80.82At1g17210838292zinc ion bindingF:zinc ion binding;P:unknown;C:cytosol, nucleus, phragmoplast;OMPFBAO.I.H.G.S.X.
0.157.80.83At1g75850843918VPS35B (VPS35 HOMOLOG B)F:unknown;P:intracellular protein transport, retrograde transport, endosome to Golgi;C:cellular_component unknown;MFOPBO.I.H.G.S.X.
0.146.80.82At5g66030836733ATGRIPInvolved in golgi protein trafficking. AtARL1 binds directly to the GRIP domain of AtGRIP in a GTP-dependent manner. Localized to the golgi apparatus, tyrosine 717 in AtGRIP is crucial for Golgi localization.O.I.H.G.S.X.
0.146.80.82At1g05090839327dentin sialophosphoprotein-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BMOFPAVO.I.H.G.S.X.
0.146.80.82At1g08620837384transcription factorF:transcription factor activity;P:regulation of transcription;C:nucleus;MFPOO.I.H.G.S.X.
0.135.80.82At3g27670822389RST1 (RESURRECTION1)A novel protein, did not show high similarity to any protein of known function; reveals a novel genetic connection between lipid synthesis and embryo development. Expressed in all tissues examined including leaves, flowers, roots, stems, and siliques, but accumulation levels were not correlated with the degree to which different organs appeared affected by the mutation. Mutant plants showed alterations in the cuticular wax profiles and embryo development.O.I.H.G.S.X.
0.135.80.81At3g51630824326WNK5 (WITH NO LYSINE (K) KINASE 5)Encodes a member of the WNK family (9 members in all) of protein kinases, the structural design of which is clearly distinct from those of other known protein kinases, such as receptor-like kinases and mitogen-activated protein kinases.O.I.H.G.S.X.
0.135.80.82At1g09730837501Ulp1 protease family proteinF:cysteine-type peptidase activity;P:proteolysis;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.135.80.81At1g59650842255CW14Encodes CW14.O.I.H.G.S.X.
0.135.80.83At4g38350829992hedgehog receptorF:hedgehog receptor activity;P:unknown;C:plasma membrane, vacuole, membrane;MOFPBAO.I.H.G.S.X.
0.124.90.82At2g31510817709IBR domain-containing protein / ARIADNE-like protein ARI7 (ARI7)F:protein binding, zinc ion binding, nucleic acid binding;P:unknown;C:unknown;MOFPVO.I.H.G.S.X.
0.114.10.82At2g39340818519SAC3/GANP family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPBVAO.I.H.G.S.X.
0.114.10.81At4g18140827539phosphataseF:phosphatase activity;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.103.40.82At1g31600840048oxidoreductase, 2OG-Fe(II) oxygenase family proteinF:oxidoreductase activity, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MOPBFVO.I.H.G.S.X.
0.103.40.81At5g07940830688-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFBPAO.I.H.G.S.X.
0.082.30.82At1g54370841878NHX5F:sodium:hydrogen antiporter activity, sodium ion transmembrane transporter activity;P:lithium ion transport, sodium ion transport;C:integral to membrane;BMOPFAO.I.H.G.S.X.
0.082.30.81At3g03380821268DegP7 (DegP protease 7)Encodes a putative DegP protease.O.I.H.G.S.X.
0.061.40.81At5g46150834657LEM3 (ligand-effect modulator 3) family protein / CDC50 family proteinF:molecular_function unknown;P:biological_process unknown;C:membrane;MOFPO.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
38.999.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
37.499.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.599.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
33.299.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
33.099.7GSM184900Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
30.299.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.699.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.599.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.499.7GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
29.299.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.299.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.099.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.199.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.999.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.699.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.499.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.099.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.899.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.299.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.199.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.099.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.599.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
25.399.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.499.6GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.599.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
19.899.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.199.6GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
18.999.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.499.5GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.499.4E-ATMX-1-raw-cel-1112746095
13.899.4GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.799.4GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
12.499.3GSM67086Arabidopsis_Stigma02GSE3056Arabidopsis Pollination StudyLink to GEO
12.399.3GSM184917Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.999.3GSM184898Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.699.3GSM67087Arabidopsis_Stigma03GSE3056Arabidopsis Pollination StudyLink to GEO
9.699.1E-MEXP-807-raw-cel-1173273144
9.599.1GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.299.1GSM184899Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.199.1E-MEXP-285-raw-cel-440782725
9.099.1E-MEXP-807-raw-cel-1173273252
8.799.0E-MEXP-509-raw-cel-829148561
8.799.0GSM133760Lindsey_1-12_heart-stage-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0381GO:0015857The directed movement of uracil, 2,4-dioxopyrimidine, into, out of, within or between cells.Link to AmiGO
0.0381GO:0042906The directed movement of xanthine into, out of, within or between cells. Xanthine (2,6-dihydroxypurine) is a purine formed in the metabolic breakdown of guanine, but is not present in nucleic acids.Link to AmiGO
0.0381GO:0045739Any process that activates or increases the frequency, rate or extent of DNA repair.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.032104140Regulation of autophagyLink to KEGG PATHWAY
0.022100562Inositol phosphate metabolismLink to KEGG PATHWAY
0.022104070Phosphatidylinositol signaling systemLink 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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