Co-expression analysis

Gene ID At1g31410
Gene name putrescine-binding periplasmic protein-related
Module size 71 genes
NF 0.37
%ile 51.1



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
0.9095.11.00At1g31410840031putrescine-binding periplasmic protein-relatedF:transporter activity;P:transport;C:chloroplast;BOPAO.I.H.G.S.X.
0.6176.70.91At1g23360838945UbiE/COQ5 methyltransferase family proteinF:methyltransferase activity;P:unknown;C:chloroplast;BOAFMPO.I.H.G.S.X.
0.5873.80.90At3g46100823753ATHRS1 (HISTIDYL-TRNA SYNTHETASE 1)histidyl-tRNA synthetaseO.I.H.G.S.X.
0.5469.50.90At2g04360814975unknown proteinF:molecular_function unknown;P:unknown;C:chloroplast;BPOO.I.H.G.S.X.
0.5368.60.91At1g06820837193CRTISO (CAROTENOID ISOMERASE)Encodes carotenoid isomerase. Catalyzes the isomerization of poly-cis-carotenoids to all-trans-carotenoids. Together with PDS and ZDS, CRTiso is required to complete the synthesis of lycopene from phytoene.O.I.H.G.S.X.
0.5267.40.91At3g02660821282emb2768 (EMBRYO DEFECTIVE 2768)F:RNA binding, tyrosine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding;P:embryonic development ending in seed dormancy, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast;OBFMPAO.I.H.G.S.X.
0.5267.40.90At4g28706828990pfkB-type carbohydrate kinase family proteinF:kinase activity, ribokinase activity;P:D-ribose metabolic process;C:chloroplast;BOMPAFO.I.H.G.S.X.
0.5166.30.91At2g26930817234ATCDPMEK (4-(CYTIDINE 5'-PHOSPHO)-2-C-METHYL-D-ERITHRITOL KINASE)Encodes a 4-(cytidine 5'-phospho)-2-C-methyl-D-erithritol kinase.O.I.H.G.S.X.
0.5065.30.91At3g60620825233phosphatidate cytidylyltransferase family proteinF:phosphatidate cytidylyltransferase activity, transferase activity, transferring phosphorus-containing groups;P:phospholipid biosynthetic process;C:chloroplast, membrane, chloroplast envelope;BOMFPO.I.H.G.S.X.
0.4862.50.90At5g48830834941unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;BPOO.I.H.G.S.X.
0.4862.50.90At1g19800838568TGD1 (TRIGALACTOSYLDIACYLGLYCEROL 1)Encodes a permease-Like protein involved in lipid transfer from the ER to the chloroplast, more specifically, transfer of phosphatidate across the chloroplast inner membrane. Mutant leaves accumulate trigalactosyldiacylglycerol, triacylglycerol and phosphatidate. Chloroplast lipids are altered in their fatty acid composition and as a consequence the development of chloroplasts in the mutants are impacted. The mutant seeds has a higher abortion rate.O.I.H.G.S.X.
0.4862.50.91At5g15390831391tRNA/rRNA methyltransferase (SpoU) family proteinF:RNA binding, RNA methyltransferase activity;P:RNA processing;C:chloroplast;BOMPFAO.I.H.G.S.X.
0.4761.20.90At4g33520829490PAA1 (P-TYPE ATP-ASE 1)Encodes a putative metal-transporting P-type ATPase.O.I.H.G.S.X.
0.4659.80.90At5g04710830349aspartyl aminopeptidase, putativeF:aminopeptidase activity, zinc ion binding;P:proteolysis;C:chloroplast, vacuole;BOFMPAO.I.H.G.S.X.
0.4659.80.91At1g25290839113ATRBL10 (ARABIDOPSIS RHOMBOID-LIKE PROTEIN 10)F:molecular_function unknown;P:biological_process unknown;C:integral to membrane;BOMPFAO.I.H.G.S.X.
0.4558.30.92At5g53860835467emb2737 (embryo defective 2737)F:unknown;P:embryonic development ending in seed dormancy;C:chloroplast;PO.I.H.G.S.X.
0.4558.30.90At1g33290840224sporulation protein-relatedF:nucleoside-triphosphatase activity, nucleotide binding;P:unknown;C:unknown;BOPMAO.I.H.G.S.X.
0.4457.20.90At5g42130834218mitochondrial substrate carrier family proteinF:binding;P:transport, mitochondrial transport;C:mitochondrial inner membrane, chloroplast;MFPOO.I.H.G.S.X.
0.4457.20.90At2g41720818771EMB2654 (EMBRYO DEFECTIVE 2654)F:unknown;P:embryonic development ending in seed dormancy;C:unknown;POMFBAO.I.H.G.S.X.
0.4355.30.90At2g15290816018TIC21 (TRANSLOCON AT INNER MEMBRANE OF CHLOROPLASTS 21)Encodes a protein located in the chloroplast inner envelope. The study of mutant defective in the gene product suggests that the protein is involved in the translocation of protein across the envelope membrane into the chloroplast stroma.O.I.H.G.S.X.
0.4355.30.91At2g35450818110catalytic/ hydrolaseF:hydrolase activity, catalytic activity;P:metabolic process;C:chloroplast;BOPMFO.I.H.G.S.X.
0.4253.90.90At5g4642083468516S rRNA processing protein RimM familyF:ribosome binding, nucleotidyltransferase activity;P:metabolic process, rRNA processing, ribosome biogenesis;C:chloroplast;BOMFPO.I.H.G.S.X.
0.4253.90.90At3g12080820382emb2738 (embryo defective 2738)F:GTP binding;P:embryonic development ending in seed dormancy;C:chloroplast;BOMFPAO.I.H.G.S.X.
0.4253.90.90At3g48110823966EDD1 (EMBRYO-DEFECTIVE-DEVELOPMENT 1)glycine-tRNA ligaseO.I.H.G.S.X.
0.4253.90.90At4g29750829097RNA bindingF:RNA binding;P:unknown;C:chloroplast;PMOFAO.I.H.G.S.X.
0.4253.90.91At3g59870825157unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;OBPO.I.H.G.S.X.
0.4253.90.91At5g36170833614HCF109 (HIGH CHLOROPHYLL FLUORESCENT 109)Required for normal processing of polycistronic plastidial transcriptsO.I.H.G.S.X.
0.4253.90.90At4g05090825853inositol monophosphatase family proteinF:3'(2'),5'-bisphosphate nucleotidase activity, inositol or phosphatidylinositol phosphatase activity;P:sulfur metabolic process;C:chloroplast;BOFPMAO.I.H.G.S.X.
0.4152.40.91At3g02450821139cell division protein ftsH, putativeF:in 6 functions;P:unknown;C:integral to membrane, chloroplast;BOMFPAVO.I.H.G.S.X.
0.4152.40.90At3g51140824278-F:unknown;P:biological_process unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;BPOO.I.H.G.S.X.
0.4152.40.90At4g21190827867emb1417 (embryo defective 1417)F:molecular_function unknown;P:embryonic development ending in seed dormancy;C:unknown;POMBO.I.H.G.S.X.
0.4152.40.90At4g20960827843cytidine/deoxycytidylate deaminase family proteinencodes diaminohydroxyphosphoribosylaminopyrimidine deaminase catalyzing the second step in the riboflavin biosynthesisO.I.H.G.S.X.
0.4152.40.90At3g20320821576TGD2 (TRIGALACTOSYLDIACYLGLYCEROL2)Encodes a permease-like component of an ABC transporter involved in lipid transfer from ER to chloroplast. A phosphatidic acid-binding protein with a predicted mycobacterial cell entry domain. It is tethered to the inner chloroplast envelope membrane facing the outer envelope membrane. Presumed bacterial orthologs of TGD1 and TGD2 in Gram-negative bacteria are typically organized in transcriptional units, suggesting their involvement in a common biological process.O.I.H.G.S.X.
0.4050.80.90At5g12130831086PDE149 (PIGMENT DEFECTIVE 149)F:unknown;P:thylakoid membrane organization;C:chloroplast thylakoid membrane, integral to membrane;BOPAMO.I.H.G.S.X.
0.4050.80.90At1g11870837734SRS (SERYL-TRNA SYNTHETASE)Seryl-tRNA synthetase targeted to chloroplasts and mitochondria. Its inactivation causes developmental arrest of chloroplasts and mitochondria in Nicotiana benthamiana.O.I.H.G.S.X.
0.3948.40.91At5g03910830269ATATH12member of ATH subfamilyO.I.H.G.S.X.
0.3948.40.90At3g20930821642RNA recognition motif (RRM)-containing proteinF:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:chloroplast;MPFOBAO.I.H.G.S.X.
0.3948.40.90At1g53120841746RNA-binding S4 domain-containing proteinF:RNA binding;P:biological_process unknown;C:chloroplast;BOPMO.I.H.G.S.X.
0.3948.40.90At1g80600844399WIN1 (HOPW1-1-INTERACTING 1)Encodes HopW1-1-Interacting protein 1 (WIN1). Interacts with the P. syringae effector HopW1-1. WIN1 is a putative acetylornithine transaminase. Modulates plant defenses against bacteria. Three WIN proteins are identified so far (WIN1: AT1G80600; WIN2: AT4G31750; WIN3: AT5G13320).O.I.H.G.S.X.
0.3846.70.90At3g06950819880tRNA pseudouridine synthase family proteinF:pseudouridine synthase activity;P:tRNA processing, pseudouridine synthesis;C:chloroplast;BOMFAPO.I.H.G.S.X.
0.3846.70.90At3g13490820551OVA5 (OVULE ABORTION 5)Encodes a dual targeted lysyl-tRNA ligase that is found both in the mitochondrion and the chloroplast. Plants mutated in this gene exhibit an ovule abortion phenotype.O.I.H.G.S.X.
0.3745.00.90At2g26540817195HEMDF:uroporphyrinogen-III synthase activity;P:tetrapyrrole biosynthetic process, porphyrin biosynthetic process;C:chloroplast;BOPAFO.I.H.G.S.X.
0.3643.60.90At5g14460831297pseudouridine synthase/ transporterF:pseudouridine synthase activity, transporter activity;P:tRNA processing, pseudouridine synthesis, RNA modification, tRNA pseudouridine synthesis;C:chloroplast;BOMFAPO.I.H.G.S.X.
0.3643.60.90At3g57560824923aspartate/glutamate/uridylate kinase family proteinencodes a N-acetylglutamate kinase, involved in arginine biosynthesisO.I.H.G.S.X.
0.3541.60.90At2g19940816513N-acetyl-gamma-glutamyl-phosphate reductase/ NAD or NADH binding / binding / catalytic/ oxidoreductase, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / protein dimerizationF:in 6 functions;P:amino acid metabolic process, response to cadmium ion;C:nucleolus, chloroplast stroma, chloroplast, membrane;BOAFPO.I.H.G.S.X.
0.3541.60.91At5g19370832057rhodanese-like domain-containing protein / PPIC-type PPIASE domain-containing proteinF:isomerase activity;P:biological_process unknown;C:chloroplast;BOMFPAO.I.H.G.S.X.
0.3541.60.91At4g15110827177CYP97B3member of CYP97BO.I.H.G.S.X.
0.3439.80.90At3g57990824968unknown proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OPFMBO.I.H.G.S.X.
0.3439.80.91At3g05350819699aminopeptidase/ hydrolaseF:hydrolase activity, aminopeptidase activity;P:proteolysis, cellular process;C:chloroplast, chloroplast stroma;BOMFAPO.I.H.G.S.X.
0.3439.80.90At3g43540823446unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;BOPO.I.H.G.S.X.
0.3439.80.90At1g36320840539unknown proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;POO.I.H.G.S.X.
0.3338.10.90At4g36390829791radical SAM domain-containing protein / TRAM domain-containing proteinF:iron-sulfur cluster binding, catalytic activity;P:biological_process unknown;C:chloroplast;OBMAPO.I.H.G.S.X.
0.3338.10.91At5g13120831151peptidyl-prolyl cis-trans isomerase cyclophilin-type family proteinF:peptidyl-prolyl cis-trans isomerase activity;P:protein folding;C:thylakoid, thylakoid lumen, chloroplast thylakoid membrane, chloroplast thylakoid lumen, chloroplast;OBMFPAVO.I.H.G.S.X.
0.3235.70.90At1g32200840112ATS1Encodes a chloroplast glycerol-3-phosphate acyltransferase.Involved in the biosynthesis of chloroplast phosphatidylglycerol.O.I.H.G.S.X.
0.3235.70.90At5g06340830522ATNUDX27 (ARABIDOPSIS THALIANA NUDIX HYDROLASE HOMOLOG 27)F:bis(5'-adenosyl)-pentaphosphatase activity, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity;P:biological_process unknown;C:chloroplast;OBPMAO.I.H.G.S.X.
0.3133.80.90At5g12150831088pleckstrin homology (PH) domain-containing protein / RhoGAP domain-containing proteinEncodes a protein with similarity to REN1, a Rho GTPase activating protein.O.I.H.G.S.X.
0.3133.80.90At3g07670819958SET domain-containing proteinF:[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity;P:biological_process unknown;C:chloroplast;MFPOO.I.H.G.S.X.
0.3032.10.90At1g15730838142PRLI-interacting factor L, putativeF:unknown;P:unknown;C:unknown;OBMFPAVO.I.H.G.S.X.
0.3032.10.90At4g09620826547-F:molecular_function unknown;P:biological_process unknown;C:chloroplast;POO.I.H.G.S.X.
0.3032.10.90At1g02910839350LPA1 (LOW PSII ACCUMULATION1)Mutants defective in this gene were shown to have a reduced PSII content (overall reduction in the levels of several PSII subunits) and a disrupted grana stack structure. The N-terminal half of the protein contains two tetratricopeptide repeat (TPR) motifs that are arranged tandemly, each consisting of a 34-residue degenerate consensus sequence. The N-terminal sequence is rich in positive and hydroxylated amino acid residues.O.I.H.G.S.X.
0.3032.10.90At1g31500840040endonuclease/exonuclease/phosphatase family proteinF:hydrolase activity;P:biological_process unknown;C:cellular_component unknown;MFOPBO.I.H.G.S.X.
0.2930.30.90At1g02150839577pentatricopeptide (PPR) repeat-containing proteinF:binding;P:unknown;C:chloroplast;POFMBO.I.H.G.S.X.
0.2930.30.90At1g32500840144ATNAP6 (NON-INTRINSIC ABC PROTEIN 6)Encodes a member of a heterogenous group of non-intrinsic ATP-binding cassette (ABC) proteins. Members of this group bear no close resemblance to each other nor to representatives of specific ABC protein subfamilies from other organisms. This grouping is arbitrary and will likely change upon acquisition of further data.O.I.H.G.S.X.
0.2830.30.90At1g54350841876ABC transporter family proteinF:ATPase activity, coupled to transmembrane movement of substances;P:transport;C:chloroplast;BOMFAPVO.I.H.G.S.X.
0.2624.40.90At1g12410837797CLP2 (CLP PROTEASE PROTEOLYTIC SUBUNIT 2)Encodes a ClpP-related sequence. Though similar to ClpP proteins, this does not contains the highly conserved catalytic triad of Ser-type proteases (Ser-His-Asp). The name reflects nomenclature described in Adam et. al (2001).O.I.H.G.S.X.
0.2624.40.90At5g63890836509ATHDH (HISTIDINOL DEHYDROGENASE)Encodes histidinol dehydrogenase. Up-regulated in response to UV-B.O.I.H.G.S.X.
0.2624.40.90At5g42765834286-F:unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast;PO.I.H.G.S.X.
0.2522.60.90At1g08520837374CHLDF:magnesium chelatase activity, nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:chlorophyll biosynthetic process;C:magnesium chelatase complex, chloroplast;MOBFPVAO.I.H.G.S.X.
0.2420.70.90At4g14910827149imidazoleglycerol-phosphate dehydratase, putativeF:imidazoleglycerol-phosphate dehydratase activity;P:histidine biosynthetic process;C:chloroplast;BOFAPMO.I.H.G.S.X.
0.2319.30.90At5g22830832346ATMGT10 (MAGNESIUM (MG) TRANSPORTER 10)putative Mg(2+) transport proteinO.I.H.G.S.X.
0.2217.50.90At5g57930835904APO2 (ACCUMULATION OF PHOTOSYSTEM ONE 2)ACCUMULATION OF PHOTOSYSTEM ONE 2O.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
58.699.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
45.899.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.399.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.299.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
42.499.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.599.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
40.299.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
39.599.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.999.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
38.599.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.399.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
38.399.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.999.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.799.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.399.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.599.7GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
32.199.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.599.7GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.099.7GSM133775Lindsey_1-27_torpedo-meristem_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
28.899.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
22.099.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.999.5GSM133781Lindsey_1-6_globular-basal_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
17.399.5GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.799.4GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.799.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
13.399.4GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
13.099.4GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
11.099.2GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.999.2E-ATMX-35-raw-cel-1574334832
10.499.2GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
10.099.2GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
8.799.0GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
8.699.0E-ATMX-35-raw-cel-1574334816

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0452GO:0001522The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.Link to AmiGO
0.0452GO:0010027A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the thylakoid membrane.Link to AmiGO
0.0402GO:0048481The process whose specific outcome is the progression of the ovule over time, from its formation to the mature structure. The ovule is the structure in seed plants enclosing the female gametophyte, and is composed of the nucellus, one or two integuments, and the funiculus; it develops into the seed.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.085500970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY
0.050300330Arginine and proline metabolismLink to KEGG PATHWAY
0.047200340Histidine 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



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