Co-expression analysis

Gene ID At5g52920
Gene name PKP-BETA1 (PLASTIDIC PYRUVATE KINASE BETA SUBUNIT 1)
Module size 15 genes
NF 0.46
%ile 65.1



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
0.7284.81.00At5g52920835369PKP-BETA1 (PLASTIDIC PYRUVATE KINASE BETA SUBUNIT 1)encodes a dominant chloroplast pyruvate kinase beta subunit. Important for seed oil biosynthesis. Ubiquitously expressed, with significantly increased expression in maturing seeds. The mutant plant has wrinkled seeds, with a 50-70% reduction in seed fatty acid content.O.I.H.G.S.X.
0.6478.90.93At5g35360833497CAC2Encodes biotin carboxylase subunit (CAC2).O.I.H.G.S.X.
0.5873.80.88At2g05990815152MOD1 (MOSAIC DEATH 1)Encodes enoyl-ACP reductase a component of the fatty acid synthase complex. A reduced function mutation in this gene, mod1, was found in a screen for premature cell death mutants. Mutant plants have reduced lipid level and pleiotropic morphological defects, including chlorotic and abnormally shaped leaves.O.I.H.G.S.X.
0.5368.60.90At1g01090839429PDH-E1 ALPHA (PYRUVATE DEHYDROGENASE E1 ALPHA)pyruvate dehydrogenase E1 alpha subunitO.I.H.G.S.X.
0.5065.30.88At2g34590818024transketolase family proteinF:pyruvate dehydrogenase (acetyl-transferring) activity, transketolase activity;P:pollen tube development;C:chloroplast, chloroplast envelope;BOMPFAO.I.H.G.S.X.
0.4862.50.88At5g10160830880beta-hydroxyacyl-ACP dehydratase, putativeF:hydro-lyase activity, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity;P:fatty acid biosynthetic process;C:cell wall, chloroplast, membrane;BOPMO.I.H.G.S.X.
0.4761.20.88At2g43360818937BIO2 (BIOTIN AUXOTROPH 2)Catalyzes the conversion of dethiobiotin to biotin.O.I.H.G.S.X.
0.4659.80.90At5g46290834671KAS I (3-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE I)3-ketoacyl-acyl carrier protein synthase I (KAS I) mRNA,O.I.H.G.S.X.
0.4457.20.88At3g25860822181LTA2Nuclear encoded dihydrolipoamide S-acetyltransferase (LTA2) that encodes teh Pyruvate Decarboxylase E2 subunit. Mutant has embryo defect.O.I.H.G.S.X.
0.4152.40.87At2g26640817205KCS11 (3-KETOACYL-COA SYNTHASE 11)Encodes KCS11, a member of the 3-ketoacyl-CoA synthase family involved in the biosynthesis of VLCFA (very long chain fatty acids).O.I.H.G.S.X.
0.4050.80.88At2g30200817570[acyl-carrier-protein] S-malonyltransferase/ binding / catalytic/ transferaseF:binding, transferase activity, [acyl-carrier-protein] S-malonyltransferase activity, catalytic activity;P:fatty acid biosynthetic process, metabolic process;C:chloroplast, chloroplast stroma;BOFMPO.I.H.G.S.X.
0.3643.60.89At1g30120839891PDH-E1 BETA (PYRUVATE DEHYDROGENASE E1 BETA)Encodes a putative plastid pyruvate dehydrogenase E1 beta subunit that is distinct from the mitochondrial pyruvate dehydrogenase E1 beta subunit.O.I.H.G.S.X.
0.3541.60.90At3g56130824779biotin/lipoyl attachment domain-containing proteinF:binding;P:unknown;C:chloroplast;BOPAFO.I.H.G.S.X.
0.3439.80.89At3g22960821870PKP-ALPHAencodes a chloroplast pyruvate kinase alpha subunit. Important for seed oil biosynthesis. Ubiquitously expressed, with significantly increased expression in maturing seeds.O.I.H.G.S.X.
0.3338.10.90At5g49820835045emb1879 (embryo defective 1879)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:cellular_component unknown;PMFOO.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
236.2100.0GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
103.799.9GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
70.699.9GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
65.099.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
64.199.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
63.199.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
55.999.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
55.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
54.299.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.699.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.899.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.199.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.099.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.199.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
46.799.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.899.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.699.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.199.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.999.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.299.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.099.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.899.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.599.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
26.399.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.699.6GSM284385Arabidopsis GEP6GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
22.599.6GSM311274Laser 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
21.699.6GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
20.699.6GSM311273Laser 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
20.199.6E-MEXP-546-raw-cel-863289424
20.099.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
19.199.6E-ATMX-30-raw-cel-1513696906
16.399.5E-MEXP-1112-raw-cel-1590665325
15.899.5GSM284384Arabidopsis GEP5GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.999.4GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.699.3GSM311288Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
11.899.3E-MEXP-1112-raw-cel-1590665377
11.399.3E-MEXP-546-raw-cel-863289532
11.199.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.999.2GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.599.2GSM131329AtGen_6-3621_Saltstress-Roots-24.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
10.399.2E-MEXP-1112-raw-cel-1590665793
10.399.2GSM311289Laser 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
10.099.2E-MEXP-1112-raw-cel-1590665273
9.799.1E-MEXP-1112-raw-cel-1590665689
9.699.1E-MEXP-1112-raw-cel-1590665741
9.099.1GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
8.799.0GSM311287Laser capture microdissected (LCM) embryo proper at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
8.699.0GSM184552Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1927GO:0006633The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.Link to AmiGO
0.1181GO:0006086The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.Link to AmiGO
0.1111GO:0009102The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.162300650Butanoate metabolismLink to KEGG PATHWAY
0.158300061Fatty acid biosynthesisLink to KEGG PATHWAY
0.130300290Valine, leucine and isoleucine biosynthesisLink to KEGG PATHWAY
0.100400620Pyruvate 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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