Co-expression analysis

Gene ID At3g24450
Gene name copper-binding family protein
Module size 19 genes
NF 0.18
%ile 15.8



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
1.00100.01.00At3g24450822035copper-binding family proteinF:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:endomembrane system;POMO.I.H.G.S.X.
0.3133.80.69At2g03240814853-F:unknown;P:unknown;C:integral to membrane;MFPOO.I.H.G.S.X.
0.2830.30.70At5g15580831411LNG1 (LONGIFOLIA1)Encodes LONGIFOLIA1 (LNG1). Regulates leaf morphology by promoting cell expansion in the leaf-length direction. The LNG1 homologue LNG2 (At3g02170) has similar function.O.I.H.G.S.X.
0.2319.30.69At5g54200835508WD-40 repeat family proteinF:signal transducer activity;P:signal transduction;C:heterotrimeric G-protein complex;MFBOPAVO.I.H.G.S.X.
0.2014.40.70At1g14350837997FLP (FOUR LIPS)Encodes a putative MYB transcription factor involved in stomata development, loss of FLP activity results in a failure of guard mother cells (GMCs) to adopt the guard cell fate, thus they continue to divide resulting in abnormal stomata consisting of clusters of numerous guard cell-like cells. This phenotype is enhanced in double mutants with MYB88.O.I.H.G.S.X.
0.2014.40.68At5g51350835209leucine-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:plasma membrane;PMOBFAVO.I.H.G.S.X.
0.1710.20.70At4g14720827125PPD2PPD2 (and its paralog, PPD1) encode plant-specific putative DNA-binding proteins. Deletion of the PPD locus increases leaf lamina size and results in dome-shaped rather than flat leaves. Siliques are also altered in shape because of extra lamina growth.O.I.H.G.S.X.
0.146.80.68At1g19870838575iqd32 (IQ-domain 32)F:calmodulin binding;P:biological_process unknown;C:cytosol, nucleus, plasma membrane, chloroplast envelope;MOFBPVAO.I.H.G.S.X.
0.146.80.69At4g33130829450-F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PO.I.H.G.S.X.
0.146.80.69At5g59010836018protein kinase-relatedF:protein tyrosine kinase activity, binding, protein kinase activity, ATP binding;P:protein amino acid phosphorylation, N-terminal protein myristoylation;C:plasma membrane;PMBOFVAO.I.H.G.S.X.
0.124.90.70At3g52890824455KIPK (KCBP-interacting protein kinase)KCBP-interacting protein kinase interacts specifically with the tail region of KCBPO.I.H.G.S.X.
0.114.10.69At1g01510839401AN (ANGUSTIFOLIA)Encodes a homolog of human CtBP. Mutant has longer and thicker leaves than wild type. Involved in controlling polar cell expansion in the leaf width direction.O.I.H.G.S.X.
0.114.10.68At5g41060834108zinc finger (DHHC type) family proteinF:zinc ion binding;P:unknown;C:plasma membrane;MOFPO.I.H.G.S.X.
0.103.40.70At4g38570830014PIS2 (PROBABLE CDP-DIACYLGLYCEROL--INOSITOL 3-PHOSPHATIDYLTRANSFERASE 2)F:phosphotransferase activity, for other substituted phosphate groups;P:phosphatidylinositol biosynthetic process;C:endomembrane system, membrane;BOMFPAO.I.H.G.S.X.
0.103.40.69At5g23430832409transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOBPAVO.I.H.G.S.X.
0.092.80.68At5g47750834826D6PKL2 (D6 PROTEIN KINASE LIKE 2)F:kinase activity;P:protein amino acid phosphorylation;C:nucleolus, nucleus, cytoplasm;MOPFBVAO.I.H.G.S.X.
0.082.30.69At3g50780824242-F:unknown;P:biological_process unknown;C:cellular_component unknown;PMOO.I.H.G.S.X.
0.071.90.69At4g27060828814TOR1 (TORTIFOLIA 1)Encodes a novel, plant-specific microtubule-associated protein that regulates the orientation of cortical microtubules and the direction of organ growth. The protein plays a role in control of microtubule dependent anisotropic cell elongation. spr2 mutant rosette leaves, cauline leaves, roots, petioles and petals curl in an anticlockwise direction.O.I.H.G.S.X.
0.051.10.70At5g05080830390UBC22 (ubiquitin-conjugating enzyme 22)F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:cellular_component unknown;MFOPVO.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
72.799.9GSM311279Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
66.899.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.599.8GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
42.099.8GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
37.499.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.999.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
35.699.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.299.7GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
34.499.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.799.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.699.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.499.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.499.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.199.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.199.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.099.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.999.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.099.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.799.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.999.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.899.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
28.299.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.599.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.399.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.299.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.099.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.699.6GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.599.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
23.999.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.199.6GSM311280Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
21.999.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
21.299.6GSM184893Arabidopsis, root cells, columella root cap, standard conditions, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
20.199.6GSM311291Laser 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
18.799.5GSM184892Arabidopsis, root cells, columella root cap, standard conditions, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
17.999.5GSM184894Arabidopsis, root cells, columella root cap, standard conditions, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
16.499.5GSM266668Arabidopsis, root cells, columella root cap, -Fe, replicate 3GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
14.199.4GSM311292Laser 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
13.399.4GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.999.3GSM184912Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.599.3GSM266667Arabidopsis, root cells, columella root cap, -Fe, replicate 2GSE10501Expression analysis of root cell-types after iron deficiency (-Fe) treatmentLink to GEO
11.499.3GSM133759Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.699.2GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.799.1GSM184911Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
9.699.1GSM184910Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0951GO:0042814Polarized growth from one end of a cell.Link to AmiGO
0.0911GO:0006661The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.Link to AmiGO
0.0871GO:0010031The organismal movement by which the tip of a plant organ follows a spiral pattern as a consequence of growth.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.041100564Glycerophospholipid metabolismLink to KEGG PATHWAY
0.036100562Inositol phosphate metabolismLink to KEGG PATHWAY
0.036104070Phosphatidylinositol 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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