Co-expression analysis

Gene ID At4g05330
Gene name AGD13 (ARF-GAP domain 13)
Module size 47 genes
NF 0.75
%ile 91.9



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
0.8089.81.00At4g05330825881AGD13 (ARF-GAP domain 13)A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes.O.I.H.G.S.X.
0.9195.60.97At1g68110843139epsin N-terminal homology (ENTH) domain-containing protein / clathrin assembly protein-relatedF:phospholipid binding, clathrin binding, binding, phosphatidylinositol binding;P:clathrin coat assembly;C:clathrin coat;PMFOO.I.H.G.S.X.
0.8693.10.97At3g09530820110ATEXO70H3 (exocyst subunit EXO70 family protein H3)A member of EXO70 gene family, putative exocyst subunits, conserved in land plants. Arabidopsis thaliana contains 23 putative EXO70 genes, which can be classified into eight clusters on the phylogenetic tree.O.I.H.G.S.X.
0.8693.10.97At2g31500817708CPK24member of Calcium Dependent Protein KinaseO.I.H.G.S.X.
0.8592.40.96At5g50830835155unknown proteinF:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;OMFBPVAO.I.H.G.S.X.
0.8592.40.97At3g05610819727pectinesterase family proteinF:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:cell wall, plant-type cell wall;OBPFMVAO.I.H.G.S.X.
0.8592.40.97At5g20410832163MGD2Encodes a type B monogalactosyldiacylglycerol (MGDG) synthase. Strongly induced by phosphate deprivation, and in non-photosynthetic tissues. Does not contribute to galactolipid synthesis under Pi-sufficient conditions but does under Pi starvation.O.I.H.G.S.X.
0.8491.90.97At1g04470839512-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBO.I.H.G.S.X.
0.8491.90.97At1g14420838004AT59F:lyase activity, pectate lyase activity;P:plant-type cell wall organization;C:endomembrane system;PBFOO.I.H.G.S.X.
0.8491.90.97At2g18470816362protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:chloroplast;MOPBFVAO.I.H.G.S.X.
0.8391.40.97At2g26410817181Iqd4 (IQ-domain 4)F:calmodulin binding;P:unknown;C:unknown;PMOBVFAO.I.H.G.S.X.
0.8391.40.97At3g54800824645pleckstrin homology (PH) domain-containing protein / lipid-binding START domain-containing proteinF:phosphoinositide binding;P:signal transduction;C:unknown;POMO.I.H.G.S.X.
0.8391.40.96At2g23900816922glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family proteinF:polygalacturonase activity;P:carbohydrate metabolic process;C:endomembrane system;PFBOMAO.I.H.G.S.X.
0.8391.40.96At4g36490829801SFH12 (SEC14-LIKE 12)F:phosphatidylinositol transporter activity, transporter activity;P:transport;C:unknown;MPFOO.I.H.G.S.X.
0.8290.90.97At3g20580821605COBL10 (COBRA-LIKE PROTEIN 10 PRECURSOR)F:unknown;P:biological_process unknown;C:anchored to membrane;PO.I.H.G.S.X.
0.8290.90.97At2g26450817185pectinesterase family proteinF:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:cell wall, plant-type cell wall;PBFMOO.I.H.G.S.X.
0.8290.90.97At5g23270832391STP11 (SUGAR TRANSPORTER 11)F:carbohydrate transmembrane transporter activity, sugar:hydrogen symporter activity;P:transport, transmembrane transport;C:integral to membrane, membrane;BFMPOAO.I.H.G.S.X.
0.8190.40.96At2g02720814801pectate lyase family proteinF:lyase activity, pectate lyase activity;P:biological_process unknown;C:endomembrane system;BPFOO.I.H.G.S.X.
0.8190.40.97At5g28680832975protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVAO.I.H.G.S.X.
0.8089.80.97At1g18990838480unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MOPFBVAO.I.H.G.S.X.
0.8089.80.96At2g27180817260unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.8089.80.96At5g39880833985unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.7888.60.97At1g55560842005sks14 (SKU5 Similar 14)F:oxidoreductase activity, copper ion binding;P:unknown;C:endomembrane system;FBPMOAO.I.H.G.S.X.
0.7888.60.97At2g13350815821C2 domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PFO.I.H.G.S.X.
0.7788.00.96At3g20190821563leucine-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:unknown;PMOFBVAO.I.H.G.S.X.
0.7687.40.96At3g62710825445glycosyl hydrolase family 3 proteinF:xylan 1,4-beta-xylosidase activity, hydrolase activity, hydrolyzing O-glycosyl compounds;P:carbohydrate metabolic process;C:endomembrane system;BOFPAMO.I.H.G.S.X.
0.7586.90.96At5g15140831366aldose 1-epimerase family proteinF:aldose 1-epimerase activity;P:galactose metabolic process, hexose metabolic process, carbohydrate metabolic process;C:endomembrane system;OBMFPVAO.I.H.G.S.X.
0.7586.90.97At1g04540839498C2 domain-containing proteinF:unknown;P:biological_process unknown;C:membrane;PMOFBO.I.H.G.S.X.
0.7486.10.97At5g15600831412SP1L4 (SPIRAL1-LIKE4)SPIRAL1-LIKE4 belongs to a six-member gene family in Arabidopsis; all members share high sequence similarity in amino- and carboxy-terminal regions. Regulates cortical microtubule organization. Mutant plants exhibit altered patterns of root, leaf and petal growth as a result of defective anisotropic cell expansion.O.I.H.G.S.X.
0.7385.50.97At3g56600824827inositol or phosphatidylinositol kinase/ phosphotransferase, alcohol group as acceptorF:inositol or phosphatidylinositol kinase activity, phosphotransferase activity, alcohol group as acceptor;P:biological_process unknown;C:unknown;PMOFBO.I.H.G.S.X.
0.7284.80.96At3g02970821168EXL6 (EXORDIUM LIKE 6)F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.I.H.G.S.X.
0.7184.20.97At2g46210819228delta-8 sphingolipid desaturase, putativeF:oxidoreductase activity, oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water, iron ion binding, heme binding;P:fatty acid biosynthetic process, lipid metabolic process;C:unknown;FMOPBVAO.I.H.G.S.X.
0.7184.20.96At3g43120823371auxin-responsive protein-relatedF:calmodulin binding;P:response to auxin stimulus;C:cellular_component unknown;POO.I.H.G.S.X.
0.7083.50.97At2g07040815274PRK2APollen receptor kinase. Coexpression of AtPRK2a with AtRopGEF12 resulted in isotropic pollen tube growth.O.I.H.G.S.X.
0.6982.90.97At3g06260819800GATL4 (Galacturonosyltransferase-like 4)Encodes a protein with putative galacturonosyltransferase activity.O.I.H.G.S.X.
0.6882.20.97At4g27790828892calcium-binding EF hand family proteinF:calcium ion binding;P:biological_process unknown;C:endomembrane system;MPFOBO.I.H.G.S.X.
0.6882.20.96At5g16500831511protein kinase family proteinF:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MOPBFVAO.I.H.G.S.X.
0.6781.60.97At3g04700819628unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.6680.10.97At5g12000831073kinaseF:kinase activity;P:protein amino acid phosphorylation;C:unknown;MPOBFVAO.I.H.G.S.X.
0.6680.10.97At4g04930825832DES-1-LIKEEncodes a sphingolipid delta4-desaturase, involved in sphingolipid biosynthesis. Specifically expressed in floral tissues. Knockout mutants were devoid of sphinga-4,8-dienine in floral tissues.O.I.H.G.S.X.
0.6680.10.96At1g58120842179unknown proteinF:unknown;P:unknown;C:unknown;PO.I.H.G.S.X.
0.6478.90.97At5g39420833938cdc2cAt (Arabidopsis thaliana cdc2c)F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:unknown;MPOFBVAO.I.H.G.S.X.
0.6277.30.96At5g47000834746peroxidase, putativeF:xylan 1,4-beta-xylosidase activity, peroxidase activity;P:response to oxidative stress;C:endomembrane system;PFOBMO.I.H.G.S.X.
0.6176.70.96At3g17060820963pectinesterase family proteinF:pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFMO.I.H.G.S.X.
0.6176.70.96At5g58170835929SVL5 (SHV3-LIKE 5)F:phosphoric diester hydrolase activity, glycerophosphodiester phosphodiesterase activity;P:glycerol metabolic process, lipid metabolic process;C:anchored to membrane;BPOMFO.I.H.G.S.X.
0.5873.80.97At1g70790843416C2 domain-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFOO.I.H.G.S.X.
0.5570.60.96At1g25240839107epsin N-terminal homology (ENTH) domain-containing protein / clathrin assembly protein-relatedF:phospholipid binding, clathrin binding, binding, phosphatidylinositol binding;P:clathrin coat assembly;C:clathrin coat, mitochondrion;PMFBAOO.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
81.799.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
73.499.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
59.599.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.599.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
49.299.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
44.199.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.399.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.099.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.399.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.599.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.499.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.999.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.799.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.399.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.699.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.399.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.299.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.199.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.999.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.099.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.299.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
30.099.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.599.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
25.599.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
24.599.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.099.5GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
18.899.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.999.3GSM133768Lindsey_1-20_torpedo-basal_Rep5_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.399.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.499.2GSM106915opr3_JA_22 hrs_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.499.1GSM284388Arabidopsis GMPE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.099.1GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
8.799.0GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0662GO:0048268The process by which clathrin triskelia are assembled into the ordered structure known as a clathrin cage.Link to AmiGO
0.0553GO:0042545The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.Link to AmiGO
0.0411GO:0019374The chemical reactions and pathways involving galactolipids, any glycolipid containing one of more residues of galactose and/or N-acetylgalactosamine.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.035100600Sphingolipid metabolismLink to KEGG PATHWAY
0.032100561Glycerolipid metabolismLink to KEGG PATHWAY
0.016100360Phenylalanine 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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