Co-expression analysis

Gene ID At5g09450
Gene name pentatricopeptide (PPR) repeat-containing protein
Module size 28 genes
NF 0.24
%ile 25.1



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
1.00100.01.00At5g09450830804pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFO.I.H.G.S.X.
0.4050.80.92At4g00660828042DEAD/DEAH box helicase, putativeF:helicase activity, nucleic acid binding, ATP binding, ATP-dependent helicase activity;P:unknown;C:unknown;BOMFPAVO.I.H.G.S.X.
0.3541.60.93At5g19680832088leucine-rich repeat family proteinF:protein binding;P:biological_process unknown;C:cellular_component unknown;MBOPFVAO.I.H.G.S.X.
0.3338.10.93At3g07140819900GPI transamidase component Gpi16 subunit family proteinF:GPI-anchor transamidase activity;P:biological_process unknown;C:endoplasmic reticulum;MFPOO.I.H.G.S.X.
0.3133.80.92At4g24490828551protein prenyltransferaseF:protein prenyltransferase activity;P:response to cadmium ion;C:unknown;MOFBPAVO.I.H.G.S.X.
0.3133.80.93At2g34970818061eIF4-gamma/eIF5/eIF2-epsilon domain-containing proteinF:binding, transferase activity, translation initiation factor activity, nucleotidyltransferase activity;P:biosynthetic process, regulation of translational initiation;C:unknown;BOMAFPO.I.H.G.S.X.
0.3032.10.92At1g18070838387EF-1-alpha-related GTP-binding protein, putativeF:translation factor activity, nucleic acid binding, GTP binding, translation release factor activity, GTPase activity;P:translational termination;C:vacuole;BMOFPAO.I.H.G.S.X.
0.3032.10.93At1g12920837850ERF1-2 (EUKARYOTIC RELEASE FACTOR 1-2)Encodes a eukaryotic release factor one homolog.O.I.H.G.S.X.
0.3032.10.92At4g30890829213UBP24 (UBIQUITIN-SPECIFIC PROTEASE 24)Encodes a ubiquitin-specific protease.O.I.H.G.S.X.
0.3032.10.92At5g28850833004calcium-binding EF hand family proteinF:calcium ion binding;P:biological_process unknown;C:endomembrane system;MOPFO.I.H.G.S.X.
0.2930.30.92At2g32920817854ATPDIL2-3 (PDI-LIKE 2-3)Encodes a protein disulfide isomerase-like (PDIL) protein, a member of a multigene family within the thioredoxin (TRX) superfamily. Transcript levels for this gene are up-regulated in response to three different chemical inducers of ER stress (dithiothreitol, beta-mercaptoethanol, and tunicamycin). AtIRE1-2 does not appear to be required for this response, but the atbzip60 mutant has a diminished response.O.I.H.G.S.X.
0.2624.40.92At3g61240825296DEAD/DEAH box helicase, putative (RH12)F:helicase activity, ATP-dependent helicase activity, ATP binding, nucleic acid binding;P:unknown;C:unknown;OBMFPAVO.I.H.G.S.X.
0.2624.40.92At3g20970821647NFU4Encodes a protein containing the NFU domain that may be involved in iron-sulfur cluster assembly. Part of a five member gene family, more closely related to NFU5 than to NFU1,2, and 3. Targeted to the mitochondrion.O.I.H.G.S.X.
0.2624.40.92At3g59990825169MAP2B (METHIONINE AMINOPEPTIDASE 2B)Encodes a MAP2 like methionine aminopeptidaseO.I.H.G.S.X.
0.2522.60.92At2g19080816425metaxin-relatedF:molecular_function unknown;P:protein targeting to mitochondrion;C:mitochondrial outer membrane, mitochondrion, mitochondrial inner membrane, plastid;MBPFOO.I.H.G.S.X.
0.2522.60.93At5g27540832814MIRO1 (Miro-related GTP-ase 1)Encodes a protein with similarity to GTPases that is localized to the mitochondrion. Involved in embryogenesis, pollen tube growth and required for mitochondrial development.O.I.H.G.S.X.
0.2522.60.92At4g04950825835thioredoxin family proteinF:electron carrier activity, protein disulfide oxidoreductase activity;P:cell redox homeostasis;C:unknown;BOMPFAVO.I.H.G.S.X.
0.2319.30.92At1g79090844250unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOBO.I.H.G.S.X.
0.2319.30.92At4g19210827661ATRLI2member of RLI subfamilyO.I.H.G.S.X.
0.2115.80.92At5g35430833507bindingF:binding;P:biological_process unknown;C:cellular_component unknown;MPOBFO.I.H.G.S.X.
0.2115.80.92At4g31480829275coatomer beta subunit, putative / beta-coat protein, putative / beta-COP, putativeF:protein binding, clathrin binding, structural molecule activity, binding;P:intracellular protein transport, vesicle-mediated transport;C:membrane coat, endomembrane system, COPI vesicle coat;MOFPO.I.H.G.S.X.
0.2014.40.92At4g26310828737elongation factor P (EF-P) family proteinF:translation elongation factor activity;P:translational elongation;C:unknown;BOPAO.I.H.G.S.X.
0.1912.70.92At3g01360821158unknown proteinF:molecular_function unknown;P:unknown;C:unknown;POO.I.H.G.S.X.
0.157.80.92At1g80930844433MIF4G domain-containing protein / MA3 domain-containing proteinF:protein binding, RNA binding, binding;P:translation, RNA metabolic process;C:cytosol, nucleus;MOFBPVAO.I.H.G.S.X.
0.157.80.92At1g70190843355ribosomal protein L12 family proteinF:structural constituent of ribosome;P:translation;C:mitochondrion, large ribosomal subunit;BOPMFO.I.H.G.S.X.
0.146.80.92At5g4562083460226S proteasome regulatory subunit, putative (RPN9)F:molecular_function unknown;P:ubiquitin-dependent protein catabolic process;C:proteasome regulatory particle, lid subcomplex;MFOPO.I.H.G.S.X.
0.135.80.93At4g12590826872unknown proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion, endoplasmic reticulum;MFOPO.I.H.G.S.X.
0.092.80.92At1g20770838667unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPFO.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
73.499.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
70.099.9GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
68.199.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
67.899.9GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
64.599.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
63.599.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
61.199.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
60.399.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
59.799.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
55.799.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
55.499.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
53.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
52.099.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
51.299.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
51.299.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
50.699.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.899.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.599.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
48.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.699.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
43.899.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.199.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.699.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
39.399.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.999.6GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
20.999.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.999.6GSM131325AtGen_6-3521_Saltstress-Roots-12.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
18.399.5GSM131321AtGen_6-3421_Saltstress-Roots-6.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
16.299.5GSM133774Lindsey_1-26_torpedo-meristem_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.799.4GSM131329AtGen_6-3621_Saltstress-Roots-24.0h_Rep1GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
14.199.4GSM131322AtGen_6-3422_Saltstress-Roots-6.0h_Rep2GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
13.499.4GSM13779Dexamethasone plus cycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
12.199.3GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.099.3GSM184923Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
11.499.3GSM131330AtGen_6-3622_Saltstress-Roots-24.0h_Rep2GSE5623AtGenExpress: Stress Treatments (Salt stress)Link to GEO
11.099.2GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
10.699.2GSM13783Dexamethasone plus cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
10.599.2GSM133962Fukuda_1-7_6A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
9.899.1GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
9.799.1GSM133963Fukuda_1-8_6B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
9.499.1GSM13780CycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
9.399.1E-MEXP-807-raw-cel-1173273116

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0982GO:0006415The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).Link to AmiGO
0.0611GO:0016485The posttranslational modification, which may include cleavage of peptide bonds, of a protein, leading to the attainment of the full functional capacity of the protein. Protein processing particularly affects secretory proteins and proteins targeted for membranes or specific cellular locations.Link to AmiGO
0.0571GO:0007005A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.079303018RNA degradationLink to KEGG PATHWAY
0.023103050ProteasomeLink 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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