Co-expression analysis

Gene ID At3g44260
Gene name CCR4-NOT transcription complex protein, putative
Module size 16 genes
NF 0.60
%ile 82.0



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
0.5673.01.00At3g44260823551CCR4-NOT transcription complex protein, putativeF:ribonuclease activity, nucleic acid binding;P:response to biotic stimulus, response to wounding, RNA modification;C:nucleus;MPOFO.I.H.G.S.X.
0.7788.00.80At5g66640836796DAR3 (DA1-RELATED PROTEIN 3)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMBFO.I.H.G.S.X.
0.7284.80.85At5g61900836311BON1 (BONZAI 1)Encodes a plasma-membrane localized, copine-like protein, which is a member of a newly identified class of calcium-dependent, phospholipid binding proteins that are present in a wide range of organisms. Mutants exhibit temperature-sensitive growth defects and increased hypersensitive response where permissive conditions are low temperature (22 degrees Celsius) and low humidity. Gene is expressed at 22 but not at 28 (restrictive condition) degrees. Lethality of double mutants with BON3 can be partially suppressed by SNC1. Double mutants show defects in development that are genetically separable from hypersensitive/cell death response.O.I.H.G.S.X.
0.7083.50.84At5g47220834768ERF2 (ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 2)Encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family (ATERF-2). The protein contains one AP2 domain. Functions as activator of GCC box–dependent transcription. Positive regulator of JA-responsive defense genes and resistance to F. oxysporum and enhances JA inhibition of root elongation.O.I.H.G.S.X.
0.6781.60.82At3g50930824257BCS1 (CYTOCHROME BC1 SYNTHESIS)F:nucleoside-triphosphatase activity, ATPase activity, nucleotide binding, ATP binding;P:unknown;C:mitochondrion, plastid;BOMFPAVO.I.H.G.S.X.
0.6781.60.83At5g42380834244CML37 (CALMODULIN LIKE 37)F:calcium ion binding;P:response to ozone;C:chloroplast;MPOFBVO.I.H.G.S.X.
0.6378.10.84At5g52050835280MATE efflux protein-relatedF:drug transporter activity, antiporter activity;P:multidrug transport;C:membrane;BOPFAMO.I.H.G.S.X.
0.6277.30.82At5g52760835353heavy-metal-associated domain-containing proteinF:metal ion binding;P:metal ion transport;C:cellular_component unknown;PO.I.H.G.S.X.
0.6176.70.86At1g35210840410unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;POO.I.H.G.S.X.
0.6176.70.83At2g32140817773transmembrane receptorF:transmembrane receptor activity;P:signal transduction, defense response, innate immune response;C:intrinsic to membrane, chloroplast;PBOO.I.H.G.S.X.
0.5873.80.83At2g44840819093ERF13 (ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR 13)encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5.O.I.H.G.S.X.
0.5673.00.82At2g27310817274F-box family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.5570.60.85At2g41640818762transferase, transferring glycosyl groupsF:transferase activity, transferring glycosyl groups;P:biological_process unknown;C:unknown;PMOBFO.I.H.G.S.X.
0.5469.50.80At2g37430818319zinc finger (C2H2 type) family protein (ZAT11)F:transcription factor activity, zinc ion binding, nucleic acid binding;P:response to chitin, regulation of transcription;C:intracellular;MPOFO.I.H.G.S.X.
0.5166.30.82At5g66620836794DAR6 (DA1-RELATED PROTEIN 6)F:zinc ion binding;P:unknown;C:unknown;MOBFPVAO.I.H.G.S.X.
0.5166.30.80At1g30370839917lipase class 3 family proteinF:triacylglycerol lipase activity;P:lipid metabolic process;C:unknown;PBOFMVO.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
105.699.9GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
70.499.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
59.299.8GSM133755Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
57.699.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
55.899.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
54.099.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.999.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.599.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.799.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.699.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.599.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.499.8GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
43.899.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
41.999.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.399.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.099.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.299.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
36.999.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.399.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.099.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
32.499.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.699.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.499.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.299.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
26.499.7GSM142624MC002_ATH1_A1.2-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
25.899.7GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
22.299.6GSM142641MC002_ATH1_A7.1-dubos-wLhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
21.599.6GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
20.599.6GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.899.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.199.6GSM142643MC002_ATH1_A7.3-dubos-wLhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
17.999.5GSM133776Lindsey_1-1_globular-apical_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
17.599.5GSM142631MC002_ATH1_A3.3-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
16.999.5GSM142642MC002_ATH1_A7.2-dubos-wLhGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
16.999.5GSM133303RIKEN-NAKABAYASHI1AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
16.399.5GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.299.5E-MEXP-849-raw-cel-1181980982
15.299.4GSM133779Lindsey_1-5_globular-basal_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.199.4GSM142644MC002_ATH1_A8.1-dubos-aihGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
15.199.4GSM131377AtGen_6-5521_Genotoxicstress-Roots-12.0h_Rep1GSE5625AtGenExpress: Stress Treatments (Genotoxic stress)Link to GEO
14.999.4GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.799.4GSM131705ATGE_83_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
14.499.4GSM131706ATGE_84_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
14.499.4GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
14.299.4GSM131703ATGE_83_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
13.899.4GSM142649MC002_ATH1_A9.3-dubos-aahGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
13.699.4GSM142648MC002_ATH1_A9.2-dubos-aahGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
13.299.4GSM311273Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
13.199.4GSM284387Arabidopsis GSUS4bGSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
12.999.3GSM184539Whole roots 2hr KCl control treated then frozen, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
12.799.3GSM284384Arabidopsis GEP5GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
12.799.3GSM311274Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
12.699.3GSM131707ATGE_84_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
12.199.3GSM131701ATGE_82_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.999.3GSM142646MC002_ATH1_A8.3-dubos-aihGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.899.3GSM142630MC002_ATH1_A3.2-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.799.3GSM142647MC002_ATH1_A9.1-dubos-aahGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.799.3GSM142634MC002_ATH1_A4.3-dubos-6kcGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.799.3GSM142633MC002_ATH1_A4.2-dubos-6kcGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.699.3GSM311291Laser 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
11.599.3GSM284385Arabidopsis GEP6GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
11.599.3GSM131702ATGE_82_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.499.3GSM131700ATGE_82_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.399.3GSM142627MC002_ATH1_A2.2-dubos-wtcGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.299.2GSM131708ATGE_84_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.199.2GSM131704ATGE_83_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
11.099.2GSM133117RIKEN-YAMAUCHI1AGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
10.999.2GSM142623MC002_ATH1_A1.1-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.499.2GSM131325AtGen_6-3521_Saltstress-Roots-12.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
10.399.2GSM142628MC002_ATH1_A2.3-dubos-wtcGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
10.199.2GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
10.199.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.899.1GSM284395Arabidopsis GPSc1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.899.1GSM184517Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.799.1GSM311293Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
9.699.1GSM311281Laser 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
9.399.1GSM142629MC002_ATH1_A3.1-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
8.999.0GSM311285Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
8.999.0GSM131160AtGen_C-10_1-Pi-6_REP1_ATH1GSE5616AtGenExpress: Response to Phytophthora infestansLink to GEO
8.899.0E-MEXP-849-raw-cel-1181980990
8.899.0GSM311282Laser 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
8.799.0GSM131162AtGen_C-12_3-Pi-6_REP3_ATH1GSE5616AtGenExpress: Response to Phytophthora infestansLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1111GO:0009270A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a humidity stimulus, moisture in the atmosphere.Link to AmiGO
0.1111GO:0010186Any process that activates or increases the frequency, rate or extent of cellular defense response.Link to AmiGO
0.1111GO:0060548Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.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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