Co-expression analysis

Gene ID At3g59040
Gene name pentatricopeptide (PPR) repeat-containing protein
Module size 7 genes
NF 0.42
%ile 58.2



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
0.5065.31.00At3g59040825073pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;POMFBAO.I.H.G.S.X.
0.5773.80.92At3g03630821203CS26O-acetylserine (thiol) lyaseO.I.H.G.S.X.
0.5673.00.93At1g69200843251kinaseF:kinase activity;P:acetate fermentation, sucrose biosynthetic process, sucrose catabolic process, using beta-fructofuranosidase;C:nucleoid;BOPAMFO.I.H.G.S.X.
0.4761.20.93At4g09730826559DEAD/DEAH box helicase, putativeF:helicase activity, ATP-dependent helicase activity, nucleic acid binding, ATP binding;P:unknown;C:chloroplast;BOMFPAVO.I.H.G.S.X.
0.4659.80.92At1g63680842672MUREEncodes AtMurE, a homolog of the bacterial MurE that catalyze the ATP-dependent formation of UDP-N-acetylmuramic acid-tripeptide in bacterial peptidoglycan biosynthesis. Localized to plastids. AtMurE is involved in chloroplast biogenesis.O.I.H.G.S.X.
0.4253.90.92At3g54090824576pfkB-type carbohydrate kinase family proteinF:kinase activity;P:acetate fermentation, sucrose biosynthetic process, sucrose catabolic process, using beta-fructofuranosidase;C:nucleus, chloroplast, nucleoid, cytoplasm;BOPAMFO.I.H.G.S.X.
0.2522.60.94At5g64580836579AAA-type ATPase family proteinF:nucleoside-triphosphatase activity, metalloendopeptidase activity, nucleotide binding, zinc ion binding, ATP binding;P:unknown;C:chloroplast, chloroplast envelope;BOMFPAVO.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
266.7100.0GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
169.7100.0GSM133775Lindsey_1-27_torpedo-meristem_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
150.099.9GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
56.699.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
52.499.8E-ATMX-35-raw-cel-1574334832
50.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.199.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
47.099.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.599.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.999.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.999.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.299.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.399.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.199.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.899.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.399.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.099.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.899.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.599.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.899.7E-ATMX-35-raw-cel-1574334816
33.299.7E-ATMX-35-raw-cel-1574334800
31.699.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.999.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
28.999.7GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
28.199.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.199.6GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
16.799.5GSM311281Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
16.099.5GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
14.699.4GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.399.3GSM311282Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
11.099.2E-MEXP-509-raw-cel-829148561
10.999.2GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
10.899.2E-MEXP-509-raw-cel-829148525
10.099.2GSM284385Arabidopsis GEP6GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.899.1GSM184552Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.699.1GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
9.099.1E-MEXP-509-raw-cel-829148703
9.099.1GSM226538L8SBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
8.899.0GSM311285Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 1GSE12402Expression 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
0.1541GO:0006535The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.Link to AmiGO
0.1111GO:0010020The division of a chloroplast within a cell to form two or more separate chloroplast compartments. This division occurs independently of mitosis.Link to AmiGO
0.1111GO:0019344The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.077100920Sulfur metabolismLink to KEGG PATHWAY
0.061100450Selenoamino acid metabolismLink to KEGG PATHWAY
0.029100270Cysteine and methionine 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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