Co-expression analysis

Gene ID At3g54500
Gene name -
Module size 5 genes
NF 0.67
%ile 86.9



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
0.4457.21.00At3g54500824615-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBO.I.H.G.S.X.
0.8089.80.85At2g46830819296CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)Encodes a transcriptional repressor that performs overlapping functions with LHY in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis. Binds to the evening element in the promoter of TOC1 and represses TOC1 transcription. CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.O.I.H.G.S.X.
0.8089.80.83At3g09600820117myb family transcription factorF:transcription factor activity, DNA binding;P:in 9 processes;C:chloroplast;PMOFO.I.H.G.S.X.
0.6781.60.78At3g02380821298COL2 (constans-like 2)homologous to the flowering-time gene CONSTANS (CO) encoding zinc-finger proteinsO.I.H.G.S.X.
0.5773.80.79At2g31380817696STHa B-box zinc finger protein that interacts with COP1. contains a novel 11 amino acid motif at the C-terminus (also found at the N-terminus of HY5) that is involved in the COP1 interaction.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
186.0100.0GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
169.7100.0GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
139.999.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
120.999.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
98.299.9GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
72.899.9GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
71.299.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
64.199.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
61.799.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
51.799.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.699.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.799.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.899.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.399.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.999.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
28.799.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.299.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.399.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.399.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.099.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.999.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
19.499.6E-MEXP-509-raw-cel-829148561
17.699.5GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.399.5E-MEXP-509-raw-cel-829148525
14.499.4GSM106923opr3_OPDA_2 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
14.399.4E-MEXP-509-raw-cel-829148348
14.299.4GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
13.199.4GSM131105Broadley_1-3_A3-Bo-P2-phosphate-starved_Rep2_ATH1GSE5614Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)Link to GEO
12.699.3GSM131106Broadley_1-4_A4-Bo-P3-phosphate-starved_Rep3_ATH1GSE5614Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)Link to GEO
12.299.3E-MEXP-509-raw-cel-829148597
11.599.3GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
11.599.3GSM106907opr3_JA_0.5 hr_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
10.799.2GSM106825opr3_0 hr_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
10.299.2GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.999.1GSM142738DH001_ATH1_A5-BCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.899.1GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.799.1GSM106922opr3_OPDA_2 hrs_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.599.1GSM106827opr3_0 hr_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.399.1GSM106910opr3_JA_2 hrs_rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.299.1E-MEXP-509-raw-cel-829148456
8.799.0GSM106919opr3_OPDA_0.5 hr_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
8.699.0GSM311278Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.3331GO:0010243A 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 an organic nitrogen stimulus. An organic nitrogen compound is formally a compound containing at least one carbon-nitrogen bond.Link to AmiGO
0.2001GO:0048574A change from the vegetative to the reproductive phase as a result of detection of, or exposure to, a period of light that exceeds the critical day length. The critical day length varies between species. Although the term is long-day is used, most species actually respond to the duration of the night, so that the response will occur when a period of darkness falls short of the number of hours defined by 24 minus the critical day length.Link to AmiGO
0.0541GO:0009909Any process that modulates the frequency, rate or extent of flower development.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.059104712Circadian rhythm - plantLink 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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