Co-expression analysis

Gene ID At4g20270
Gene name BAM3 (BARELY ANY MERISTEM 3)
Module size 16 genes
NF 0.40
%ile 56.1



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
0.4152.41.00At4g20270827774BAM3 (BARELY ANY MERISTEM 3)Encodes a CLAVATA1-related receptor kinase-like protein required for both shoot and flower meristem function. It has a broad expression pattern and is involved in vascular strand development in the leaf, control of leaf shape, size and symmetry, male gametophyte development and ovule specification and function.O.I.H.G.S.X.
0.5974.70.80At3g01670821096unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;PO.I.H.G.S.X.
0.5873.80.82At1g23530838962unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POO.I.H.G.S.X.
0.5873.80.77At5g42720834281glycosyl hydrolase family 17 proteinF:cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:anchored to membrane;PFOO.I.H.G.S.X.
0.5673.00.80At5g25490832624zinc finger (Ran-binding) family proteinF:binding, zinc ion binding;P:biological_process unknown;C:intracellular;MPOFO.I.H.G.S.X.
0.5267.40.77At1g79430844281APL (ALTERED PHLOEM DEVELOPMENT)Encodes gene product that is required for several aspects of phloem development in the root: (1) the specific divisions organizing the phloem pole, (2) sieve element differentiation and (3) the expression of a companion-specific gene. Mutant has a defect in the organization of phloem poles in the root. apl seedlings have a short, determinate root with only occasional lateral branches.O.I.H.G.S.X.
0.4862.50.80At3g20570821604plastocyanin-like domain-containing proteinF:electron carrier activity, copper ion binding;P:unknown;C:anchored to membrane;POBFMVO.I.H.G.S.X.
0.4457.20.81At3g20870821636metal transporter family proteinF:metal ion transmembrane transporter activity;P:metal ion transport;C:endomembrane system, membrane;BMOAFPO.I.H.G.S.X.
0.4355.30.77At3g05620819728pectinesterase family proteinF:enzyme inhibitor activity, pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFMO.I.H.G.S.X.
0.3846.70.79At2g37590818336Dof-type zinc finger domain-containing proteinF:transcription factor activity, DNA binding;P:regulation of transcription;C:nucleus;PMOBFAO.I.H.G.S.X.
0.3745.00.79At1g13050837862-F:molecular_function unknown;P:biological_process unknown;C:unknown;PMFOBVO.I.H.G.S.X.
0.3643.60.77At3g01680821097unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.3235.70.81At1g69580843294transcription factorF:transcription factor activity;P:regulation of transcription;C:unknown;POMBO.I.H.G.S.X.
0.2930.30.79At5g05160830398leucine-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:cell wall, plasma membrane;PMOBFVAO.I.H.G.S.X.
0.2420.70.77At5g03530831810RABC2A (RAB GTPASE HOMOLOG C2A)Encodes a member of the Rab GTPase family of proteins. This protein interacts with the tail region of a myosin XI protein (AT5G43900) in a GTP-dependent manner. CFP:RabC2a appears to co-localize with peroxisomes.O.I.H.G.S.X.
0.1912.70.78At1g10380837577unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PO.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
93.499.9GSM184477Lateral Root Cap root cells 2hr KCl control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
40.399.8GSM184483Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
28.999.7GSM184480Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
25.899.7GSM184478Lateral Root Cap root cells 2hr KCl control treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
21.099.6E-MEXP-265-raw-cel-414618394
19.099.5E-MEXP-265-raw-cel-414618291
18.899.5GSM131655ATGE_27_AGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
18.499.5GSM131656ATGE_27_BGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
16.199.5E-MEXP-265-raw-cel-414618491
15.299.4GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.199.4GSM131657ATGE_27_CGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
14.799.4GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
14.699.4GSM184476Lateral Root Cap root cells 2hr KCl control treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.199.4E-MEXP-265-raw-cel-414618693
14.099.4GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.799.4GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.499.4GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.299.4GSM133753Turner_A-7-Turne-WT-Base1_SLDGSE5729Role of COV in vascular patterningLink to GEO
13.299.4GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.199.4GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
12.899.3GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
12.799.3GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
12.099.3GSM266665Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 4GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
11.999.3GSM13780CycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
11.799.3E-MEXP-1451-raw-cel-1585200362
11.699.3GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
11.699.3GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.599.3GSM13783Dexamethasone plus cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
11.399.3GSM13779Dexamethasone plus cycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
11.299.2GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.099.2GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.099.2GSM134208Murray_3-4_D7-GROWTH_Rep1_ATH1GSE5750Growth of suspension-cultured cellsLink to GEO
10.999.2E-MEXP-265-raw-cel-414618796
10.799.2GSM184907Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.699.2GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.599.2GSM184908Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
10.399.2GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
10.199.2GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.199.2GSM184481Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.699.1GSM133754Turner_A-8-Turne-WT-Base2_SLDGSE5729Role of COV in vascular patterningLink to GEO
9.699.1GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
9.599.1GSM184897Arabidopsis, root cells, cortex, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.399.1GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
9.199.1GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
8.999.0GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.999.0E-MEXP-265-raw-cel-414617783
8.999.0GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
8.999.0GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
8.899.0GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1181GO:0010088The formation of the principal food-conducting tissue of a vascular plant.Link to AmiGO
0.0871GO:0048437The process whose specific outcome is the progression of the floral organ over time, from its formation to the mature structure.Link to AmiGO
0.0741GO:0010089The formation of the principal water-conducting tissue of a vascular plant.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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