Co-expression analysis

Gene ID At3g08730
Gene name PK1 (PROTEIN-SERINE KINASE 1)
Module size 20 genes
NF 0.61
%ile 82.1



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
0.5773.81.00At3g08730820020PK1 (PROTEIN-SERINE KINASE 1)Encodes a protein-serine kinase that phosphorylates ribosomal protein in vitro. Activation of AtS6k is regulated by 1-naphthylacetic acid and kinetin, at least in part, via a lipid kinase-dependent pathway. Involved in translational up-regulation of ribosomal proteins. Phosphorylated by PDK1. Interacts with RAPTOR1, which in turn interacts with TOR. SPK6 activity is affected by osmotic stress, and plants overexpressing S6k1 are hypersensitive to osmotic stress. The gene is expressed in all tissues examined, with highest expression level detected in metabolically active tissues.O.I.H.G.S.X.
0.8290.90.91At1g10740837617unknown proteinF:unknown;P:glycerol biosynthetic process;C:endomembrane system;BOPFMO.I.H.G.S.X.
0.7586.90.91At5g47620834812heterogeneous nuclear ribonucleoprotein, putative / hnRNP, putativeF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPOFBAO.I.H.G.S.X.
0.7284.80.91At1g06700837180serine/threonine protein kinase, putativeF:protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVAO.I.H.G.S.X.
0.7184.20.90At3g12620820442protein phosphatase 2C family protein / PP2C family proteinF:protein serine/threonine phosphatase activity, catalytic activity;P:protein amino acid dephosphorylation;C:protein serine/threonine phosphatase complex;PMOFBVO.I.H.G.S.X.
0.6882.20.89At1g05960837106bindingF:binding;P:biological_process unknown;C:plasma membrane;MFPBOO.I.H.G.S.X.
0.6781.60.92At5g61960836317AML1 (ARABIDOPSIS MEI2-LIKE PROTEIN 1)A member of mei2-like gene family, predominantly plant-based family of genes encoding RNA binding proteins with characteristic presence of a highly conserved RNA binding motif first described in the mei2 gene of the fission yeast S. pombe. In silico analyses reveal nine mei2 -like genes in A. thaliana. They were grouped into four distinct clades, based on overall sequence similarity and subfamily-specific sequence elements. AML1 is a member of two sister clades of mei2-like gene family, AML1 through AML5 and belongs to the clade named ALM14. AML1 is expressed during early embryo development, particularly along embryonic axis at torpedo stage, in shoot apex (weaker expression) and in the organogenic regions of floral apices.O.I.H.G.S.X.
0.6378.10.89At3g07880819979Rho GDP-dissociation inhibitor family proteinF:Rho GDP-dissociation inhibitor activity;P:biological_process unknown;C:cytoplasm;MFPOO.I.H.G.S.X.
0.6378.10.88At2g19880816507ceramide glucosyltransferase, putativeF:ceramide glucosyltransferase activity;P:biological_process unknown;C:endomembrane system;MBPFAOO.I.H.G.S.X.
0.6277.30.87At3g62660825440GATL7 (Galacturonosyltransferase-like 7)Encodes a protein with putative galacturonosyltransferase activity.O.I.H.G.S.X.
0.6277.30.90At4g20380827786zinc finger protein (LSD1)LSD1 monitors a superoxide-dependent signal and negatively regulates a plant cell death pathway. contains zinc-finger motifs. LSD1 negatively regulates a basal defense pathway that can act upstream or independently of both NIM1/NPR1 function and SA accumulation following avirulent or virulent pathogen challengeO.I.H.G.S.X.
0.5974.70.89At5g16480831509tyrosine specific protein phosphatase family proteinF:phosphatase activity, protein tyrosine phosphatase activity, phosphoprotein phosphatase activity;P:dephosphorylation;C:cellular_component unknown;FOPBMO.I.H.G.S.X.
0.5974.70.88At1g22200838825unknown proteinF:molecular_function unknown;P:biological_process unknown;C:endoplasmic reticulum;MOFPO.I.H.G.S.X.
0.5773.80.89At3g57480824915zinc finger (C2H2 type, AN1-like) family proteinF:zinc ion binding, nucleic acid binding;P:biological_process unknown;C:intracellular;MFOPO.I.H.G.S.X.
0.5673.00.91At4g00110828145GAE3 (UDP-D-GLUCURONATE 4-EPIMERASE 3)Encodes a putative membrane-anchored UDP-D-glucuronate 4-epimerase.O.I.H.G.S.X.
0.5469.50.88At5g58950836012protein kinase family proteinF:protein serine/threonine/tyrosine kinase activity, kinase activity;P:protein amino acid phosphorylation;C:cytosol, plasma membrane;MPOFBVAO.I.H.G.S.X.
0.5166.30.90At1g10660837609unknown proteinF:unknown;P:unknown;C:endomembrane system;PMFO.I.H.G.S.X.
0.5166.30.89At3g09760820134zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMFOVBO.I.H.G.S.X.
0.4963.50.89At2g40620818657bZIP transcription factor family proteinF:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMOFBO.I.H.G.S.X.
0.4761.20.90At5g58380835951SIP1 (SOS3-INTERACTING PROTEIN 1)Encodes a CBL-interacting protein kinase with similarity to SOS protein kinase.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
59.699.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
51.999.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
47.599.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
45.299.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.099.7GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
29.399.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.399.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
28.099.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.499.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.199.7E-ATMX-1-raw-cel-1112746095
27.099.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
26.899.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.799.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.999.6GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.899.6GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.899.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.399.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
24.299.6GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.399.6GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.399.6GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
23.199.6GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
21.099.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
21.099.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.999.6GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.899.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
20.699.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.499.5GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
15.899.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.699.5GSM239252Columbia glabrous (C24) wild type stamenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
12.999.3GSM311289Laser 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
10.099.2GSM284396Arabidopsis GPSc2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.899.1GSM142906WW002_ATH1_A2-willa-ISOX-REP2GSE6181Assembly of the cell wall pectic matrix.Link to GEO
9.699.1GSM142907WW002_ATH1_A2-willa-ISOX-REP3GSE6181Assembly of the cell wall pectic matrix.Link to GEO
9.399.1GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.199.1GSM284390Arabidopsis GPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.099.1GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0951GO:0010602Regulation of the chemical reactions and pathways involving 1-aminocyclopropane-1-carboxylate, the anion of 1-aminocyclopropane-1-carboxylic acid, a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene (ethene), a fruit-ripening hormone in plants.Link to AmiGO
0.0951GO:0045836Any process that activates or increases the frequency, rate or extent of meiosis.Link to AmiGO
0.0911GO:0000303A 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 superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.022100520Amino sugar and nucleotide sugar metabolismLink to KEGG PATHWAY
0.019100500Starch and sucrose metabolismLink to KEGG PATHWAY
0.002101100Metabolic pathwaysLink 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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