Co-expression analysis

Gene ID At1g01060
Gene name LHY (LATE ELONGATED HYPOCOTYL)
Module size 5 genes
NF 0.74
%ile 91.4



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
1.00100.01.00At1g01060839341LHY (LATE ELONGATED HYPOCOTYL)LHY encodes a myb-related putative transcription factor involved in circadian rhythm along with another myb transcription factor CCA1O.I.H.G.S.X.
0.8693.10.81At3g09600820117myb family transcription factorF:transcription factor activity, DNA binding;P:in 9 processes;C:chloroplast;PMOFO.I.H.G.S.X.
0.8089.80.83At2g46830819296CCA1 (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.
0.6781.60.80At3g02380821298COL2 (constans-like 2)homologous to the flowering-time gene CONSTANS (CO) encoding zinc-finger proteinsO.I.H.G.S.X.
0.4457.20.77At3g54500824615-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBO.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
116.499.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
55.999.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.199.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.299.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.899.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.599.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.899.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.499.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
20.799.6GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.299.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.599.6GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
17.199.5E-MEXP-509-raw-cel-829148561
14.599.4GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.599.4E-MEXP-509-raw-cel-829148525
14.499.4GSM106923opr3_OPDA_2 hrs_Rep2GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
14.299.4GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
14.299.4GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.999.4E-MEXP-509-raw-cel-829148348
13.799.4GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.399.4GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
12.799.3GSM131105Broadley_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
12.499.3GSM131106Broadley_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
11.999.3E-MEXP-509-raw-cel-829148597
11.999.3GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
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
10.799.2GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
10.799.2GSM106825opr3_0 hr_Rep1GSE4733Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profilingLink to GEO
9.899.1GSM142735DH001_ATH1_A2-BCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.899.1GSM142738DH001_ATH1_A5-BCP2GSE6162Transcriptome 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
9.099.1GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
8.699.0GSM106919opr3_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
0.4002GO: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
0.3331GO: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
0.0633GO:0009723A 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 ethylene (ethene) stimulus.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.118204712Circadian 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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