Co-expression analysis

Gene ID At4g18510
Gene name CLE2 (CLAVATA3/ESR-RELATED)
Module size 33 genes
NF 0.28
%ile 32.3



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
1.00100.01.00At4g18510827583CLE2 (CLAVATA3/ESR-RELATED)CLE2, putative ligand, member of large gene family homologous to Clavata3O.I.H.G.S.X.
0.4558.30.74At5g59090836026ATSBT4.12F:identical protein binding, serine-type endopeptidase activity;P:proteolysis, negative regulation of catalytic activity;C:apoplast, nucleus, cytoplasm;BPOFAMO.I.H.G.S.X.
0.4253.90.63At4g28410828958aminotransferase-relatedF:1-aminocyclopropane-1-carboxylate synthase activity, pyridoxal phosphate binding, transferase activity, transferring nitrogenous groups, transaminase activity, catalytic activity;P:cellular amino acid and derivative metabolic process, biosynthetic process;C:cellular_component unknown;BOPMAFO.I.H.G.S.X.
0.3948.40.64At4g22212828313-Encodes a defensin-like (DEFL) family protein.O.I.H.G.S.X.
0.3846.70.67At3g01260821171aldose 1-epimerase/ carbohydrate binding / catalytic/ isomeraseF:carbohydrate binding, isomerase activity, aldose 1-epimerase activity, catalytic activity;P:galactose metabolic process, hexose metabolic process, carbohydrate metabolic process;C:endomembrane system;OBMFPVAO.I.H.G.S.X.
0.3745.00.61At2g28780817427unknown proteinF:unknown;P:biological_process unknown;C:mitochondrion;BPOO.I.H.G.S.X.
0.3541.60.60At4g39675830122unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.3338.10.63At5g63600836480FLS5 (FLAVONOL SYNTHASE 5)encodes a protein whose sequence is similar to flavonol synthaseO.I.H.G.S.X.
0.3338.10.64At5g10580830923unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BPOO.I.H.G.S.X.
0.3235.70.60At1g13300837890myb family transcription factorF:transcription factor activity, DNA binding;P:regulation of transcription;C:unknown;POVBMFO.I.H.G.S.X.
0.3235.70.74At2g31085817664CLE6 (CLAVATA3/ESR-RELATED 6)Member of a large family of putative ligands homologous to the Clavata3 gene. Consists of a single exon. Can replace CLV3 function in vivo.O.I.H.G.S.X.
0.3032.10.60At3g25930822190universal stress protein (USP) family proteinF:molecular_function unknown;P:response to stress;C:cellular_component unknown;PO.I.H.G.S.X.
0.2930.30.60At4g15400827208transferase family proteinF:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:unknown;C:cellular_component unknown;PFBO.I.H.G.S.X.
0.2930.30.62At3g21770821731peroxidase 30 (PER30) (P30) (PRXR9)F:transferase activity, transferring glycosyl groups, peroxidase activity;P:response to oxidative stress;C:cell wall, nucleus, cytoplasm, plant-type cell wall;PFOBMO.I.H.G.S.X.
0.2830.30.60At5g52790835356CBS domain-containing protein-relatedF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BOMFPAO.I.H.G.S.X.
0.2830.30.62At2g44380819045DC1 domain-containing proteinF:unknown;P:unknown;C:unknown;PMOO.I.H.G.S.X.
0.2726.20.64At1g50560841477CYP705A25member of CYP705AO.I.H.G.S.X.
0.2726.20.62At2g35000818064zinc finger (C3HC4-type RING finger) family proteinE3 ligase-like protein induced by chitin oligomers.O.I.H.G.S.X.
0.2624.40.61At2g32270817787ZIP3A member of Zrt- and Irt-related protein (ZIP) family. transcript is induced in response to zinc deficiency in the root. also response to iron deficiency.O.I.H.G.S.X.
0.2522.60.61At4g17800827502DNA-binding protein-relatedF:unknown;P:biological_process unknown;C:cellular_component unknown;PBMOFO.I.H.G.S.X.
0.2522.60.60At4g37060829860PLP5 (PATATIN-LIKE PROTEIN 5)F:nutrient reservoir activity;P:metabolic process, lipid metabolic process;C:cellular_component unknown;PBOMFO.I.H.G.S.X.
0.2420.70.66At4g30450829168glycine-rich proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MOBPFVAO.I.H.G.S.X.
0.2319.30.63At2g44790819088UCC2 (UCLACYANIN 2)Encodes a uclacyanin, a protein precursor that is closely related to precursors of stellacyanins and a blue copper protein from pea pods.O.I.H.G.S.X.
0.2115.80.60At1g31885840079transporterF:transporter activity;P:transport;C:integral to membrane, membrane;BPOMFAVO.I.H.G.S.X.
0.2115.80.61At4g37010829855caltractin, putative / centrin, putativeF:calcium ion binding;P:biological_process unknown;C:unknown;MFPOBO.I.H.G.S.X.
0.2014.40.61At1g61750842472-F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MPOBFVAO.I.H.G.S.X.
0.1912.70.61At1g08670837389epsin N-terminal homology (ENTH) domain-containing protein / clathrin assembly protein-relatedF:binding;P:biological_process unknown;C:cellular_component unknown;MFPOO.I.H.G.S.X.
0.1710.20.64At5g06800830570myb family transcription factorF:transcription factor activity;P:regulation of transcription;C:unknown;POFMO.I.H.G.S.X.
0.168.80.63At4g24180828519-F:molecular_function unknown;P:response to other organism;C:endomembrane system;PMFBOVO.I.H.G.S.X.
0.157.80.61At5g46890834734protease inhibitor/seed storage/lipid transfer protein (LTP) family proteinF:lipid binding;P:lipid transport;C:endomembrane system;PO.I.H.G.S.X.
0.157.80.60At4g21600828246ENDO5 (endonuclease 5)Encodes a protein with mismatch-specific endonuclease activity with a preference for T/G, A/G, and G/G of single base mismatches. It also has the ability to cleave indel types of mismatches (heteroduplexes with loops).O.I.H.G.S.X.
0.135.80.59At4g26320828738AGP13 (arabinogalactan protein 13)F:unknown;P:unknown;C:anchored to membrane;PO.I.H.G.S.X.
0.114.10.60At1g71692843497AGL12 (AGAMOUS-LIKE 12)Encodes a member of the MADS box family of transcription factors. Involved in root cell differentiation and flowering time. Loss of function mutations have abnormal cellular differentiation in the roots and are late flowering. AGL12 along with AGL14, and AGL17 is preferentially expressed in root tissues and represent the only characterized MADS box genes expressed in roots.O.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
141.599.9GSM133775Lindsey_1-27_torpedo-meristem_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
90.599.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
76.699.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
73.299.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
72.799.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
53.299.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
48.799.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.899.8GSM311282Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
47.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.199.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.899.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.599.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.499.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.399.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.899.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
42.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.999.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.199.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.899.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.399.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_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
36.299.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.799.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.199.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.199.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.699.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
28.699.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.099.6GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
16.699.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.599.5GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.899.5GSM218586Pericycle root cells 2hr continuous KNO3 and MSX and Gln treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.799.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.299.4GSM284398Arabidopsis GGSc2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.199.4GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.399.3GSM311281Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
9.299.1GSM284396Arabidopsis GPSc2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
8.799.0E-MEXP-98-raw-cel-320188969
8.799.0E-ATMX-35-raw-cel-1574334864

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0541GO:0019318The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule.Link to AmiGO
0.0531GO:0006308The chemical reactions and pathways resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.Link to AmiGO
0.0511GO:0006519The chemical reactions and pathways involving amino acids, organic acids containing one or more amino substituents, and compounds derived from amino acids, as carried out by individual cells.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.018100360Phenylalanine metabolismLink to KEGG PATHWAY
0.018100680Methane metabolismLink to KEGG PATHWAY
0.015100940Phenylpropanoid biosynthesisLink 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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