Co-expression analysis

Gene ID At3g13160
Gene name pentatricopeptide (PPR) repeat-containing protein
Module size 12 genes
NF 0.48
%ile 68.5

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
0.3032.11.00At3g13160820505pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:mitochondrion, membrane;POMFBAO.I.H.G.S.X.
0.7385.50.92At1g56110842063NOP56 (Arabidopsis homolog of nucleolar protein Nop56)NOP56-like proteinO.I.H.G.S.X.
0.7083.50.94At3g18600821391DEAD/DEAH box helicase, putativeF:helicase activity, ATP binding, ATP-dependent helicase activity, nucleic acid binding;P:unknown;C:nucleolus;BOMFPAVO.I.H.G.S.X.
0.6781.60.92At5g62440836365-Encodes a protein DOMINO1 that belongs to a plant-specific gene family sharing a common motif present in the tomato DEFECTIVE CHLOROPLASTS AND LEAVES (LeDCL) protein. DOMINO1 is located in the nucleus. Arabidopsis embryos carrying the domino1 mutation grow slowly in comparison with wild type embryos and reach only the globular stage at desiccation. The primary defect of the mutation at the cellular level is the large size of the nucleolus that can be observed soon after fertilization in the nuclei of both the embryo and the endosperm. DOMINO1 might have a role in ribosome biogenesis and in determining the rate of cell division.O.I.H.G.S.X.
0.5570.60.93At4g32720829408AtLa1 (Arabidopsis thaliana La protein 1)Encodes AtLa1, a member of the highly abundant phosphoprotein La proteins. Predominantly localized to the nucleoplasm and was also detected in the nucleolar cavity. Has RNA binding activity. Required for normal ribosome biogenesis and embryogenesis.O.I.H.G.S.X.
0.5469.50.94At2g37990818377ribosome biogenesis regulatory protein (RRS1) family proteinF:unknown;P:ribosome biogenesis;C:nucleolus;MFOPBO.I.H.G.S.X.
0.5267.40.92At5g14050831254transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex;BMOFPAVO.I.H.G.S.X.
0.5267.40.92At3g11964820370RNA bindingF:RNA binding;P:mRNA processing, RNA processing;C:nucleolus, plasma membrane;BOMFPAO.I.H.G.S.X.
0.5065.30.92At5g57280835833methyltransferaseF:methyltransferase activity;P:metabolic process;C:unknown;BOMFPAO.I.H.G.S.X.
0.4862.50.92At4g04940825833transducin family protein / WD-40 repeat family proteinF:nucleotide binding;P:rRNA processing;C:CUL4 RING ubiquitin ligase complex;MFBOPAO.I.H.G.S.X.
0.4659.80.93At5g14520831303pescadillo-relatedF:transcription coactivator activity;P:cell proliferation;C:nucleolus, intracellular;MFOPO.I.H.G.S.X.
0.3439.80.92At4g28450828962nucleotide binding / protein bindingThis gene is predicted to encode a protein with a DWD motif. It can bind to DDB1a in Y2H assays and may be involved in the formation of a CUL4-based E3 ubiquitin ligaseO.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
104.299.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
98.899.9GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
88.899.9GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
73.599.9GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
72.399.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
71.999.9GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
70.499.9GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
67.199.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
66.699.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
65.499.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
63.199.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
62.499.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
61.199.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
58.599.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
58.299.8GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
57.999.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
57.599.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
57.499.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
56.699.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
56.599.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
56.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
55.599.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
54.499.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
54.199.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.099.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
25.699.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.599.6GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
16.199.5GSM154508Arabidopsis growing pollen tubes rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
12.599.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.299.2GSM131450AtGen_6-9222_Heatstress-Roots-1.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
8.999.0GSM265423Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2GSE10497Expression analysis of root developmental zones after iron deficiency (-Fe) treatmentLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1541GO:0017126The process by which the nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells, is formed and assembled.Link to AmiGO
0.1001GO:0051302Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells.Link to AmiGO
0.0561GO:0006397Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG

Inter-species module comparison

Select a plant to compare co-expressed genes between species.

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