Co-expression analysis

Gene ID At5g15980
Gene name pentatricopeptide (PPR) repeat-containing protein
Module size 64 genes
NF 0.26
%ile 28.9



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
1.00100.01.00At5g15980831455pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion;POMBFO.I.H.G.S.X.
0.4862.50.87At5g02820831314RHL2 (ROOT HAIRLESS 2)Involved in the patterning and shape of leaf trichomes. Encodes the DNA topoisomerase VI SPO11-3, involved in endoreduplicationO.I.H.G.S.X.
0.4558.30.88At1g24510839066T-complex protein 1 epsilon subunit, putative / TCP-1-epsilon, putative / chaperonin, putativeF:unfolded protein binding, protein binding, ATP binding;P:protein folding, cellular protein metabolic process;C:plasma membrane;BOMFPAO.I.H.G.S.X.
0.4355.30.89At4g35850829739pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:unknown;C:mitochondrion;POMFBAO.I.H.G.S.X.
0.3948.40.87At1g08220837343-F:molecular_function unknown;P:mitochondrial proton-transporting ATP synthase complex assembly;C:mitochondrial inner membrane;FPOAMO.I.H.G.S.X.
0.3948.40.86At3g02650821285pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFBAO.I.H.G.S.X.
0.3948.40.86At3g13860820599HSP60-3A (HEAT SHOCK PROTEIN 60-3A)F:protein binding, ATP binding;P:response to cadmium ion;C:mitochondrion, plasma membrane;BOMFPAVO.I.H.G.S.X.
0.3846.70.86At3g60880825259dihydrodipicolinate synthase 1 (DHDPS1) (DHDPS) (DHPS1)Encodes a dihydropicolinate synthase involved in lysine biosynthesis. The enzyme is allosterically inhibited by lysine. It is predicted to localize to the cholorplast.O.I.H.G.S.X.
0.3846.70.85At4g24830828586arginosuccinate synthase familyF:argininosuccinate synthase activity, ATP binding;P:arginine biosynthetic process;C:chloroplast stroma, chloroplast;OBMAFPO.I.H.G.S.X.
0.3846.70.86At1g64880842796ribosomal protein S5 family proteinF:structural constituent of ribosome, RNA binding;P:translation;C:ribosome, Golgi apparatus, intracellular;OBMFAPVO.I.H.G.S.X.
0.3745.00.86At4g02930828134elongation factor Tu, putative / EF-Tu, putativeF:translation elongation factor activity, ATP binding;P:translational elongation;C:mitochondrion, cell wall;BOMFPAVO.I.H.G.S.X.
0.3643.60.86At3g5749082491640S ribosomal protein S2 (RPS2D)F:structural constituent of ribosome;P:translation;C:cytosolic small ribosomal subunit, ribosome, intracellular, membrane;BOMAFPO.I.H.G.S.X.
0.3643.60.86At3g49080824070ribosomal protein S9 family proteinF:structural constituent of ribosome;P:translation;C:cytosolic small ribosomal subunit, ribosome, intracellular;BOMAPFVO.I.H.G.S.X.
0.3541.60.86At3g20000821538TOM40Encodes a component of the TOM receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. With TOM22, functions as the transit peptide receptor at the surface of the mitochondrial outer membrane and facilitates the movement of preproteins into the translocation pore.O.I.H.G.S.X.
0.3439.80.86At3g20050821544ATTCP-1Encodes a putative cytoplasmic chaperonin that is similar to mouse Tcp-1 (t complex polypeptide 1).O.I.H.G.S.X.
0.3439.80.86At4g2362082846250S ribosomal protein-relatedF:structural constituent of ribosome, 5S rRNA binding;P:translation;C:ribosome, intracellular;OBPO.I.H.G.S.X.
0.3338.10.85At1g73180843652eukaryotic translation initiation factor-relatedF:molecular_function unknown;P:biological_process unknown;C:plasma membrane;MFOPBO.I.H.G.S.X.
0.3338.10.87At2g20060816525ribosomal protein L4 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, intracellular, chloroplast, large ribosomal subunit;BOMFAPO.I.H.G.S.X.
0.3338.10.87At3g26410822245methyltransferase/ nucleic acid bindingF:methyltransferase activity, nucleic acid binding;P:methylation;C:endomembrane system;MAFOPBO.I.H.G.S.X.
0.3338.10.86At1g31860840076AT-IEencodes a bifunctional protein that has phosphoribosyl-ATP pyrophosphohydrolase (PRA-PH) and phosphoribosyl-AMP cyclohydrolase (PRA-CH) activities.O.I.H.G.S.X.
0.3235.70.86At3g04820819642pseudouridine synthaseF:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis, tRNA pseudouridine synthesis;C:unknown;BOMAFPO.I.H.G.S.X.
0.3235.70.86At1g48630841284RACK1B_AT (RECEPTOR FOR ACTIVATED C KINASE 1 B)Encodes a protein with similarity to mammalian RACKs. RACKs function to shuttle activated protein kinase C to different subcellular sites and may also function as a scaffold through physical interactions with other proteins. RACK1B has no phenotype on its own and probably acts redundantly with RACK1A and RACK1C.O.I.H.G.S.X.
0.3235.70.85At2g28450817393zinc finger (CCCH-type) family proteinF:methyltransferase activity, zinc ion binding, RNA methyltransferase activity, nucleic acid binding;P:acetate biosynthetic process from carbon monoxide, methanol oxidation, RNA processing;C:cellular_component unknown;BOMFAPVO.I.H.G.S.X.
0.3235.70.89At1g58380842207XW6F:structural constituent of ribosome;P:translation;C:cytosolic small ribosomal subunit, plasma membrane, chloroplast, membrane;BOMFPAVO.I.H.G.S.X.
0.3133.80.85At5g23300832394PYRD (pyrimidine d)dihydroorotate dehydrogenase, catalyses fourth step of pyrimidine biosynthesisO.I.H.G.S.X.
0.3133.80.87At1g2691083703660S ribosomal protein L10 (RPL10B)F:structural constituent of ribosome;P:translation;C:ribosome, membrane, chloroplast envelope;MOAPFBO.I.H.G.S.X.
0.3133.80.85At1g14620838024DECOY (DECOY)F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;FMPOBO.I.H.G.S.X.
0.3032.10.85At4g10480826640nascent polypeptide associated complex alpha chain protein, putative / alpha-NAC, putativeF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPABVO.I.H.G.S.X.
0.3032.10.87At1g16870838258mitochondrial 28S ribosomal protein S29-relatedF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPO.I.H.G.S.X.
0.3032.10.85At4g15640827241unknown proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion;PO.I.H.G.S.X.
0.2930.30.88At1g55890842039pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:mitochondrion;POMFBAO.I.H.G.S.X.
0.2830.30.85At3g1358082056060S ribosomal protein L7 (RPL7D)F:structural constituent of ribosome, transcription regulator activity;P:translation;C:cytosolic ribosome, cytosolic large ribosomal subunit, chloroplast, large ribosomal subunit, membrane;MOFAPO.I.H.G.S.X.
0.2830.30.86At5g41190834121-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFAPBVO.I.H.G.S.X.
0.2726.20.85At3g02530821160chaperonin, putativeF:unfolded protein binding, protein binding, ATP binding;P:response to cadmium ion;C:membrane, cytoplasm;BOMFPAO.I.H.G.S.X.
0.2726.20.87At3g18190821346chaperonin, putativeF:unfolded protein binding, protein binding, ATP binding;P:response to cadmium ion;C:unknown;BOMFPAVO.I.H.G.S.X.
0.2726.20.88At3g44330823558-F:unknown;P:protein processing;C:mitochondrion, endoplasmic reticulum, plasma membrane, vacuole;MOPABO.I.H.G.S.X.
0.2624.40.85At3g1061082023040S ribosomal protein S17 (RPS17C)F:structural constituent of ribosome;P:translation;C:cytosolic small ribosomal subunit, cytosolic ribosome, ribosome;MOAFPO.I.H.G.S.X.
0.2624.40.85At4g1317082693160S ribosomal protein L13A (RPL13aC)F:structural constituent of ribosome;P:translation;C:cytosolic large ribosomal subunit, ribosome, membrane;OMBAPFO.I.H.G.S.X.
0.2624.40.87At1g04190839442tetratricopeptide repeat (TPR)-containing proteinF:binding;P:biological_process unknown;C:cellular_component unknown;OBMPFAO.I.H.G.S.X.
0.2624.40.85At2g18400816355ribosomal protein L6 family proteinF:structural constituent of ribosome;P:translation;C:ribosome, intracellular, large ribosomal subunit;BOFPMAO.I.H.G.S.X.
0.2522.60.85At4g2589082869560S acidic ribosomal protein P3 (RPP3A)F:structural constituent of ribosome;P:translational elongation;C:cytosolic ribosome, ribosome, nucleus, plasma membrane;MPFOBO.I.H.G.S.X.
0.2522.60.86At3g1460082068860S ribosomal protein L18A (RPL18aC)F:structural constituent of ribosome;P:N-terminal protein myristoylation, translation, ribosome biogenesis;C:cytosolic ribosome, cytosolic large ribosomal subunit, ribosome, membrane;MOFPO.I.H.G.S.X.
0.2522.60.85At1g61730842470DNA-binding storekeeper protein-relatedF:transcription regulator activity;P:biological_process unknown;C:cytosol, nucleolus, chloroplast;OBMFPVAO.I.H.G.S.X.
0.2420.70.86At1g26460839187pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion;POFMO.I.H.G.S.X.
0.2319.30.86At1g1854083843560S ribosomal protein L6 (RPL6A)F:structural constituent of ribosome;P:translation;C:in 8 components;MOFPAO.I.H.G.S.X.
0.2319.30.86At3g01160820504unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cytosol, nucleus;MOFBPVAO.I.H.G.S.X.
0.2115.80.87At5g03300831882ADK2 (ADENOSINE KINASE 2)Encodes adenosine kinase 2 (ADK2), a typical, constitutively expressed housekeeping enzyme. Shows a high sequence identity with ADK1. Involved in salvage synthesis of adenylates and methyl recycling. Enzyme activity is substantially inhibited in roots, siliques and dry seeds by an unknown compound. May contribute to cytokinin interconversion.O.I.H.G.S.X.
0.2115.80.85At5g6751083688760S ribosomal protein L26 (RPL26B)F:structural constituent of ribosome;P:translation;C:cytosolic ribosome, cytosolic large ribosomal subunit, large ribosomal subunit;MAOFPBO.I.H.G.S.X.
0.2115.80.85At4g26110828717NAP1Encodes a member of a small gene family of proteins with similarity to nucleosome assembly proteins.May function in nucleotide excision repair. Loss of function mutations have no obvious visible phenotypes but do seem to affect transcription of NER related genes.O.I.H.G.S.X.
0.2014.40.90At1g53880841825GTP binding / translation initiation factorF:GTP binding, translation initiation factor activity;P:translational initiation, cellular metabolic process;C:eukaryotic translation initiation factor 2B complex;OBMFPAO.I.H.G.S.X.
0.2014.40.85At5g40660834066ATP12 protein-relatedF:protein binding;P:proton-transporting ATP synthase complex assembly;C:cellular_component unknown;BOMFPO.I.H.G.S.X.
0.2014.40.85At1g25350839120OVA9 (ovule abortion 9)F:glutamine-tRNA ligase activity;P:glutamyl-tRNA aminoacylation, translation, ovule development;C:cytosol;BOMFAPO.I.H.G.S.X.
0.1811.40.85At3g66658819849ALDH22a1 (Aldehyde Dehydrogenase 22a1)Encodes a putative aldehyde dehydrogenase. The gene is not responsive to osmotic stress and is expressed constitutively at a low level in plantlets and root cultures.O.I.H.G.S.X.
0.168.80.85At3g22480821819prefoldin-related KE2 family proteinF:unfolded protein binding;P:protein folding;C:prefoldin complex;MFOPAO.I.H.G.S.X.
0.168.80.85At1g04270839564RPS15 (CYTOSOLIC RIBOSOMAL PROTEIN S15)Encodes cytosolic ribosomal protein S15.O.I.H.G.S.X.
0.157.80.86At5g05520830435outer membrane OMP85 family proteinF:molecular_function unknown;P:biological_process unknown;C:mitochondrion, plastid;BOMFPVO.I.H.G.S.X.
0.146.80.86At1g65290842836mtACP2 (mitochondrial acyl carrier protein 2)Encodes a member of the mitochondrial acyl carrier protein (ACP) family. As part of the mitochondrial matrix, it is likely to be involved in fatty acid or lipoic acid biogenesis.O.I.H.G.S.X.
0.146.80.86At2g21160816651translocon-associated protein alpha (TRAP alpha) family proteinF:unknown;P:biological_process unknown;C:chloroplast thylakoid membrane, endoplasmic reticulum, plasma membrane, vacuole;MPFOO.I.H.G.S.X.
0.146.80.86At4g31180829246aspartyl-tRNA synthetase, putative / aspartate--tRNA ligase, putativeF:aspartate-tRNA ligase activity, nucleotide binding, aminoacyl-tRNA ligase activity, nucleic acid binding, ATP binding;P:response to cadmium ion, aspartyl-tRNA aminoacylation;C:chloroplast, cytoplasm;BOMFAPO.I.H.G.S.X.
0.135.80.86At4g26300828736emb1027 (embryo defective 1027)F:nucleotide binding, aminoacyl-tRNA ligase activity, arginine-tRNA ligase activity, ATP binding;P:embryonic development ending in seed dormancy, arginyl-tRNA aminoacylation;C:mitochondrion, chloroplast;OBMAFPVO.I.H.G.S.X.
0.135.80.85At3g27080822326TOM20-3 (TRANSLOCASE OF OUTER MEMBRANE 20 KDA SUBUNIT 3)Component of the TOM complex involved in transport of nuclear-encoded mitochondrial proteinsO.I.H.G.S.X.
0.135.80.85At1g04340839547lesion inducing protein-relatedF:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PBOO.I.H.G.S.X.
0.124.90.86At1g34020840299transporter-relatedF:unknown;P:unknown;C:plasma membrane, membrane;PMFOBO.I.H.G.S.X.
0.071.90.85At1g71070843447glycosyltransferase family 14 protein / core-2/I-branching enzyme family proteinF:transferase activity, transferring glycosyl groups, acetylglucosaminyltransferase activity;P:carbohydrate biosynthetic process;C:endomembrane system, membrane;MPBVOO.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
60.599.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
36.399.7GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
33.999.7GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
31.899.7GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.999.7GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.099.6GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
23.199.6GSM133757Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
19.899.6GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
19.899.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.799.6GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
19.599.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.899.5GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
18.799.5GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
18.799.5GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
18.299.5GSM311294Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
18.299.5GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
18.199.5GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
18.199.5GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
18.199.5GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
17.799.5GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
17.399.5GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
17.299.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.899.5GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
16.599.5GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
16.299.5GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
16.099.5GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.999.5GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.899.5GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
15.099.4GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.999.4GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.299.4GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.199.3GSM311279Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
11.699.3GSM311280Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
11.099.2GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.199.2GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
9.799.1GSM142736DH001_ATH1_A3-TCP1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.299.1GSM10481lec1-1 Mature Green Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
9.099.1GSM311293Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
8.999.0GSM10451WT Mature Green Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
8.699.0GSM10453WT Mature Green Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0532GO:0044267The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes protein modification.Link to AmiGO
0.0502GO:0006626The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.Link to AmiGO
0.0311GO:0033615The aggregation, arrangement and bonding together of a proton-transporting ATP synthase in the mitochondrial inner membrane.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.0811203010RibosomeLink to KEGG PATHWAY
0.036200970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY
0.026100340Histidine 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



Back to the CoP portal site

Back to the KAGIANA project homepage