Co-expression analysis

Gene ID At1g09530
Gene name PIF3 (PHYTOCHROME INTERACTING FACTOR 3)
Module size 6 genes
NF 0.02
%ile 0.8



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
1.00100.01.00At1g09530837479PIF3 (PHYTOCHROME INTERACTING FACTOR 3)Transcription factor interacting with photoreceptors phyA and phyB. Forms a ternary complex in vitro with G-box element of the promoters of LHY, CCA1. Acts as a negative regulator of phyB signalling. It degrades rapidly after irradiation of dark grown seedlings in a process controlled by phytochromes. Does not play a significant role in controlling light input and function of the circadian clockwork. Binds to G- and E-boxes, but not to other ACEs. Binds to anthocyanin biosynthetic genes in a light- and HY5-independent fashion. PIF3 function as a transcriptional activator can be functionally and mechanistically separated from its role in repression of PhyB mediated processes.O.I.H.G.S.X.
0.3338.10.74At5g25350832607EBF2 (EIN3-BINDING F BOX PROTEIN 2)Arabidopsis thaliana EIN3-binding F-box protein 2 (EBF2) mRNA. Part of the SCF complex, it is located in the nucleus and is involved in the ethylene-response pathway.O.I.H.G.S.X.
0.146.80.73At5g14780831330FDH (FORMATE DEHYDROGENASE)Encodes a NAD-dependent formate dehydrogenase.O.I.H.G.S.X.
0.010.20.74At5g02480831883-F:unknown;P:unknown;C:cellular_component unknown;PO.I.H.G.S.X.
0.010.20.73At3g48690824030CXE12Encodes a protein with carboxylesterase whose activity was tested using both pNA and 2,4-D-methyl.O.I.H.G.S.X.
0.010.20.73At4g18710827605BIN2 (BRASSINOSTEROID-INSENSITIVE 2)ATSK (shaggy-like kinase) family member that encodes an AtSK protein involved in the cross-talk between auxin and brassinosteroid signaling pathways. BR-INSENSITIVE 2 mutant indicated that the BR-insensitive dwarf phenotype was due to a semidominant mutation in the BIN2. BIN2 is not allelic to BRI1. BIN2-mediated phosphorylation appears to promote BZR1 export from the nucleus.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
52.699.8GSM284389Arabidopsis GMPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
52.199.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.899.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.799.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.799.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.599.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.299.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.199.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
37.599.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.399.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.299.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
36.699.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.699.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.199.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
34.299.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.199.7GSM311290Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
30.999.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.899.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.099.7GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
29.699.7GSM284391Arabidopsis GPE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
28.799.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.799.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.299.7GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
27.299.7GSM10479lec1-1 Cotyledon Stage Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
26.399.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.299.6GSM284398Arabidopsis GGSc2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
22.899.6GSM311289Laser capture microdissected (LCM) cellularized endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
21.899.6GSM284390Arabidopsis GPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
21.599.6E-MEXP-285-raw-cel-440783213
19.899.6GSM10480lec1-1 Cotyledon Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
18.899.5GSM10449WT Cotyledon Stage Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
18.599.5GSM311295Laser capture microdissected (LCM) general seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
17.999.5E-MEXP-285-raw-cel-440783152
16.199.5GSM131454AtGen_6-9322_Heatstress-Roots-3.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
15.899.5GSM131453AtGen_6-9321_Heatstress-Roots-3.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
15.899.5GSM176879AWP_Control_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
15.799.5GSM10448WT Cotyledon Stage Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
14.999.4GSM131449AtGen_6-9221_Heatstress-Roots-1.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
13.799.4GSM147964WT Globular Stage Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
13.699.4GSM131450AtGen_6-9222_Heatstress-Roots-1.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
13.299.4GSM284388Arabidopsis GMPE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
12.799.3GSM133810Diamond_A-3-Diamo-fum_SLDGSE5735Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)Link to GEO
12.599.3GSM311278Laser 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
12.499.3GSM142624MC002_ATH1_A1.2-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
12.499.3GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.499.3GSM142623MC002_ATH1_A1.1-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
12.299.3GSM142631MC002_ATH1_A3.3-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
11.799.3GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
11.399.3GSM284397Arabidopsis GGSc1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
11.399.3GSM142851MG001_ATH1_A4-Torres-2N1GSE6176Impact of Type III effectors on plant defense responsesLink to GEO
11.199.2GSM147963WT Globular Stage Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
11.199.2GSM311294Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
10.699.2GSM231197wild-type at T0.5, biological rep2GSE9148Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5hLink to GEO
10.199.2GSM147965lec1-1 Globular Stage Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
9.499.1GSM184490Epidermis&Cortex root cells 2hr transitory KNO3 treated, biological rep3GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.299.1GSM133812Diamond_A-1-Diamo-met_SLDGSE5735Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)Link to GEO
9.299.1GSM226538L8SBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
8.999.0GSM184555Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.799.0GSM231196wild-type at T0.5, biological rep1GSE9148Expression data of 10-day-old wild-type and chl1-5 plants exposed to 25 mM nitrate for 0h or 0.5hLink to GEO
8.699.0E-MEXP-1725-raw-cel-1669614634
8.699.0GSM131448AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.2861GO:0046827Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.Link to AmiGO
0.2501GO:0009729The series of events in which a brassinosteroid stimulus is received by a cell and converted into a molecular signal.Link to AmiGO
0.2501GO:0031539Any process that activates or increases the frequency, rate or extent of chemical reactions and pathways involving anthocyanins.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.057104712Circadian rhythm - plantLink to KEGG PATHWAY
0.053100630Glyoxylate and dicarboxylate metabolismLink to KEGG PATHWAY
0.023100680Methane 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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