Co-expression analysis

Gene ID At2g23150
Gene name NRAMP3 (NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 3)
Module size 20 genes
NF 0.06
%ile 3.3



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
1.00100.01.00At2g23150816847NRAMP3 (NATURAL RESISTANCE-ASSOCIATED MACROPHAGE PROTEIN 3)Encodes a member of the Nramp2 metal transporter family; like its homolog Atnramp4, localized in vacuolar membrane. Seedlings of double mutant, atnramp3-1 atnramp4-1, were arrested at early germination.O.I.H.G.S.X.
0.3235.70.74At5g60870836208regulator of chromosome condensation (RCC1) family proteinF:Ran GTPase binding;P:biological_process unknown;C:mitochondrion;MOBPFAVO.I.H.G.S.X.
0.1710.20.74At1g44960841061-F:unknown;P:biological_process unknown;C:plasma membrane;BOPAMO.I.H.G.S.X.
0.124.90.76At2g434208189433-beta hydroxysteroid dehydrogenase/isomerase family proteinF:binding, 3-beta-hydroxy-delta5-steroid dehydrogenase activity, catalytic activity;P:steroid biosynthetic process, metabolic process;C:plasma membrane;BOMPAFVO.I.H.G.S.X.
0.124.90.73At5g63010836421WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;MFOPBAO.I.H.G.S.X.
0.114.10.75At1g23890839000NHL repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BOMAPO.I.H.G.S.X.
0.103.40.74At1g74240843764mitochondrial substrate carrier family proteinF:binding;P:transport, mitochondrial transport;C:mitochondrial inner membrane, membrane;MFPOO.I.H.G.S.X.
0.082.30.73At1g20100838599unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;MOPFBVO.I.H.G.S.X.
0.082.30.76At3g48150823970APC8 (ANAPHASE-PROMOTING COMPLEX SUBUNIT 8)anaphase-promoting complex or cyclosome subunitO.I.H.G.S.X.
0.071.90.74At5g25150832586TAF5 (TBP-ASSOCIATED FACTOR 5)Encodes a putative TATA-binding-protein associated factor TAF5. TAFs are subunits of the general transcription factor IID (TFIID).O.I.H.G.S.X.
0.071.90.74At1g10240837563FRS11 (FAR1-related sequence 11)F:zinc ion binding;P:response to red or far red light;C:cellular_component unknown;PFOMO.I.H.G.S.X.
0.071.90.73At2g38660818448tetrahydrofolate dehydrogenase/cyclohydrolase, putativeF:binding, catalytic activity;P:folic acid and derivative biosynthetic process, metabolic process;C:unknown;OBMFPAO.I.H.G.S.X.
0.061.40.73At5g10270830891CDKCEncodes CDKC;1, part of a CDKC kinase complex that is targeted by Cauliflower mosaic virus (CaMV) for transcriptional activation of viral genes. Also regulates plant growth and development.O.I.H.G.S.X.
0.051.10.74At1g50940841516ETFALPHA (electron transfer flavoprotein alpha)Encodes the electron transfer flavoprotein ETF alpha, a putative subunit of the mitochondrial electron transfer flavoprotein complex (ETF beta is At5g43430.1) in Arabidopsis. Mutations of the ETF beta gene results in accelerated senescence and early death compared to wild-type during extended darkness.O.I.H.G.S.X.
0.040.90.73At5g20930832217TSL (TOUSLED)Nuclear serine/threonine protein kinase that requires a coiled-coil region for oligomerization and catalytic activity. Required for leaf and flower development. Expression localized to the developing style by stage 13.O.I.H.G.S.X.
0.040.90.73At1g51710841596UBP6 (UBIQUITIN-SPECIFIC PROTEASE 6)Ubiquitin-specific protease 6 (UBP6). Deubiquinating enzyme. Interacts with calmodulin.O.I.H.G.S.X.
0.040.90.74At1g66750842993CAK4 (CDK-ACTIVATING KINASE 4)F:protein binding, protein serine/threonine kinase activity, kinase activity;P:regulation of cyclin-dependent protein kinase activity;C:nucleus, cytoplasm;MPOFBVAO.I.H.G.S.X.
0.040.90.73At3g12180820395cornichon family proteinF:molecular_function unknown;P:intracellular signaling cascade;C:endomembrane system, membrane;MFPOO.I.H.G.S.X.
0.020.40.73At3g077508199663' exoribonuclease family domain 1-containing proteinF:3'-5'-exoribonuclease activity, RNA binding;P:RNA processing;C:cellular_component unknown;MOFAPBO.I.H.G.S.X.
0.010.20.73At3g06810819865IBR3 (IBA-RESPONSE 3)Encodes a protein with similarity to acyl-CoA dehydrogenases. Mutations in IBR3 render plants resistant to indole-3-butryic acid, a putative storage form of the biologically active auxin IAA (indole-3-acetic acid). IBR3 is hypothesized to carry out the second step in a β-oxidation-like process of IBA metabolism in Arabidopsis. Though its subcellular location has not been determined, IBR3 has a peroxisomal targeting sequence and two other putative IBA metabolic enzymes (IBR1 and IBR10) can be found in this organelle. No specific enzymatic activity has been documented for IBR3, but double mutant analyses with CHY1 argue against a role for IBR3 in general fatty acid β-oxidation.O.I.H.G.S.X.

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Link to AtGenExpress Visualization Tool



Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
90.399.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
66.399.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
66.399.8GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
59.699.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
53.399.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
41.499.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
41.299.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.599.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
36.799.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
35.199.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.399.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.999.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.499.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.099.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.799.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.599.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.799.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.599.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.199.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.399.6GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.199.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.899.6GSM133029BC482-1GSE5684AtGenExpress: Pathogen Series: Response to Botrytis cinerea infectionLink to GEO
24.599.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.099.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.999.6GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.799.6GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.399.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.099.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
18.699.5E-MEXP-1797-raw-cel-1669768057
17.999.5GSM133030BC482-2GSE5684AtGenExpress: Pathogen Series: Response to Botrytis cinerea infectionLink to GEO
17.999.5GSM131537ATGE_25_AGSE5630AtGenExpress: Developmental series (leaves)Link to GEO
17.799.5E-ATMX-31-raw-cel-1516947916
17.399.5E-MEXP-791-raw-cel-1122937569
17.299.5GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.999.5GSM131538ATGE_25_BGSE5630AtGenExpress: Developmental series (leaves)Link to GEO
16.499.5GSM131539ATGE_25_CGSE5630AtGenExpress: Developmental series (leaves)Link to GEO
16.199.5E-MEXP-1797-raw-cel-1669767976
16.099.5E-MEXP-509-raw-cel-829148703
15.799.5E-MEXP-1797-raw-cel-1669768012
14.399.4GSM133025BC181-1GSE5684AtGenExpress: Pathogen Series: Response to Botrytis cinerea infectionLink to GEO
13.099.4E-ATMX-31-raw-cel-1516947882
12.999.3GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
12.499.3E-MEXP-1797-raw-cel-1669767949
12.399.3E-ATMX-31-raw-cel-1516947899
11.699.3E-MEXP-1797-raw-cel-1669767958
11.199.2E-MEXP-1797-raw-cel-1669768075
10.299.2E-MEXP-1797-raw-cel-1669767985
10.099.2GSM133957Fukuda_1-2_0B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
10.099.2GSM142644MC002_ATH1_A8.1-dubos-aihGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.899.1GSM142646MC002_ATH1_A8.3-dubos-aihGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.899.1E-MEXP-1797-raw-cel-1669768003
9.199.1E-MEXP-1797-raw-cel-1669768048
8.899.0E-MEXP-1797-raw-cel-1669767994

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0951GO:0030071Any process that modulates the frequency, rate or extent of the onset of anaphase (chromosome movement) in the mitotic cell cycle.Link to AmiGO
0.0911GO:0000079Any process that modulates the frequency, rate or extent of CDK activity.Link to AmiGO
0.0911GO:0010670Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving dioxygen (O2), or any of the reactive oxygen species, e.g. superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (-OH).Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.054100410beta-Alanine metabolismLink to KEGG PATHWAY
0.051100640Propanoate metabolismLink to KEGG PATHWAY
0.038100071Fatty acid 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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