Co-expression analysis

Gene ID At5g24830
Gene name pentatricopeptide (PPR) repeat-containing protein
Module size 5 genes
NF 0.18
%ile 15.6



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
0.5065.31.00At5g24830832552pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:unknown;POMFBAO.I.H.G.S.X.
0.5065.30.90At5g12260831101-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POFBO.I.H.G.S.X.
0.2930.30.90At4g17020827410transcription factor-relatedF:RNA polymerase II transcription factor activity;P:DNA repair, regulation of transcription, DNA-dependent;C:endomembrane system, nucleus;MFOPO.I.H.G.S.X.
0.114.10.90At5g24710832542-F:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MOBFPVAO.I.H.G.S.X.
0.071.90.90At5g59710836092VIP2 (VIRE2 INTERACTING PROTEIN2)Encodes a nuclear-localized NOT (negative on TATA-less) domain-containing protein that interacts with the Agrobacterium VirE2 protein and is required for Agrobacterium-mediated plant transformation. It likely facilitates T-DNA integration into plant chromosomes and may play a role as a transcriptional regulator.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
392.3100.0GSM133763Lindsey_1-15_torpedo-cotyledon_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
361.0100.0GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
239.8100.0GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
172.3100.0GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
146.199.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
120.499.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
101.399.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
100.699.9E-ATMX-31-raw-cel-1516947916
66.799.8GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
65.999.8GSM133773Lindsey_1-25_torpedo-meristem_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
38.799.8GSM134206Murray_3-3_D5-GROWTH_Rep1_ATH1GSE5750Growth of suspension-cultured cellsLink to GEO
33.799.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
33.599.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.499.7GSM133957Fukuda_1-2_0B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
31.499.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
22.899.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
17.899.5GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.899.5GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.699.5GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.699.5GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.299.5GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.299.5E-ATMX-31-raw-cel-1516947899
15.999.5E-ATMX-31-raw-cel-1516947882
14.799.4GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.699.4GSM134373St.Clair_1-34_346_Cvi-1_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1GSE5753Expression Level Polymorphism Project (ELP) - Cvi-1Link to GEO
13.899.4GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.399.4GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.199.4GSM176878AWP_AL_Txed_2GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
12.199.3GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
12.099.3GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.999.3GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
11.999.3GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.999.3GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
11.699.3GSM133774Lindsey_1-26_torpedo-meristem_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.399.3GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
11.099.2GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
10.899.2GSM142907WW002_ATH1_A2-willa-ISOX-REP3GSE6181Assembly of the cell wall pectic matrix.Link to GEO
10.899.2GSM142906WW002_ATH1_A2-willa-ISOX-REP2GSE6181Assembly of the cell wall pectic matrix.Link to GEO
9.899.1GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
9.399.1GSM133771Lindsey_1-23_torpedo-apical_Rep5_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.399.1GSM252679Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep1GSE9996Organ regeneration in plants is independent of stem cell niche activityLink to GEO
8.899.0GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.2501GO:0015074The process by which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.Link to AmiGO
0.0511GO:0016481Any process that stops, prevents or reduces the frequency, rate or extent of transcription.Link to AmiGO
0.0191GO: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
0.053103022Basal transcription factorsLink to KEGG PATHWAY
0.036103420Nucleotide excision repairLink 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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