Co-expression analysis

Gene ID At1g29710
Gene name pentatricopeptide (PPR) repeat-containing protein
Module size 16 genes
NF 0.27
%ile 31.5



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
0.4659.81.00At1g29710839848pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion;POMO.I.H.G.S.X.
0.4761.20.88At4g21060827853galactosyltransferase family proteinF:transferase activity, transferring hexosyl groups, transferase activity, transferring glycosyl groups;P:protein amino acid glycosylation;C:membrane;MPOFBO.I.H.G.S.X.
0.4457.20.89At1g09820837514pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.4050.80.88At4g15820827263-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMFPBVO.I.H.G.S.X.
0.4050.80.89At5g39710833967EMB2745 (EMBRYO DEFECTIVE 2745)F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POMFBAO.I.H.G.S.X.
0.3846.70.89At5g65560836682pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.3439.80.88At4g39530830107pentatricopeptide (PPR) repeat-containing proteinF:binding;P:biological_process unknown;C:unknown;POMFBAO.I.H.G.S.X.
0.2930.30.88At1g270708395965'-AMP-activated protein kinase-relatedF:unknown;P:unknown;C:unknown;MFPOBAO.I.H.G.S.X.
0.2624.40.88At4g20740827823pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POFMABO.I.H.G.S.X.
0.2319.30.91At3g06910819876ULP1A (UB-LIKE PROTEASE 1A)Encodes a deSUMOylating enzyme. In vitro it has both peptidase activity and isopeptidase activity: it can cleave the C-terminal residues from SUMO to activate it for attachment to a target protein and it can also act on the isopeptide bond between SUMO and another protein. In vitro assays suggest that this enzyme is active against SUMO1 and SUMO2. It has weak activity with SUMO3 and cannot act on SUMO5. The N-terminal regulatory region of this protein is required for full activity.O.I.H.G.S.X.
0.2217.50.90At1g63130842617pentatricopeptide (PPR) repeat-containing proteinTransacting siRNA generating locus. Its derived siR9as targets AT1G62930 for cleavage. Itself is targeted by TAS2-derived ta-siR2140 for cleavage.O.I.H.G.S.X.
0.2217.50.88At5g48990834958kelch repeat-containing F-box family proteinencodes an F-box protein that interacts with SKP1 and likely to be involved in ubiquitin-mediated protein degradation.O.I.H.G.S.X.
0.2115.80.90At1g30290839909-unknown proteinO.I.H.G.S.X.
0.2115.80.89At5g42400834246SDG25 (SET DOMAIN PROTEIN 25)F:unknown;P:unknown;C:unknown;MOPFBAVO.I.H.G.S.X.
0.1710.20.88At5g08510830750pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFMABO.I.H.G.S.X.
0.168.80.89At2g31970817756RAD50F:zinc ion binding, ATP binding, nuclease activity;P:DNA repair;C:chromosome, Mre11 complex;MOBFPAVO.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
79.399.9GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
76.699.9GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
75.399.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
68.699.9GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
67.399.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
65.599.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
61.599.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
60.399.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
59.699.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
59.499.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
59.299.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
58.699.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
58.499.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
57.599.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
55.999.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
54.199.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
54.199.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
53.999.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
50.999.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.499.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.099.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
34.799.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
32.499.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
22.399.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
15.099.4GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
14.499.4E-MEXP-1443-raw-cel-1581869745
13.799.4E-MEXP-1443-raw-cel-1581869803
13.799.4GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.699.4GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.299.4GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.499.3GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
11.699.3GSM270868Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
11.599.3E-MEXP-1725-raw-cel-1669614634
11.599.3GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.599.3GSM270870Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
11.499.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
9.299.1GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1051GO:0016926The process by which a SUMO protein (small ubiquitin-related modifier) is cleaved from its target protein.Link to AmiGO
0.0381GO:0006486The addition of a sugar unit to a protein amino acid, e.g. the addition of glycan chains to proteins.Link to AmiGO
0.0171GO:0006281The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.083103450Non-homologous end-joiningLink to KEGG PATHWAY
0.065100310Lysine degradationLink to KEGG PATHWAY
0.049103440Homologous recombinationLink 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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