Co-expression analysis

Gene ID At4g39960
Gene name DNAJ heat shock family protein
Module size 41 genes
NF 0.36
%ile 48.3



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
1.00100.01.00At4g39960830157DNAJ heat shock family proteinF:unfolded protein binding, heat shock protein binding, ATP binding;P:protein folding, response to heat;C:chloroplast thylakoid membrane, chloroplast;OBMFPAVO.I.H.G.S.X.
0.6075.70.91At5g54180835506PTAC15 (PLASTID TRANSCRIPTIONALLY ACTIVE15)F:molecular_function unknown;P:biological_process unknown;C:plastid chromosome, chloroplast, nucleoid;PMOO.I.H.G.S.X.
0.5974.70.92At2g31170817673SYCO ARATHF:cysteine-tRNA ligase activity, nucleotide binding, aminoacyl-tRNA ligase activity, ATP binding;P:cysteinyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast;OBMAFPVO.I.H.G.S.X.
0.5873.80.94At1g01970839299pentatricopeptide (PPR) repeat-containing proteinF:molecular_function unknown;P:biological_process unknown;C:unknown;POMFO.I.H.G.S.X.
0.4761.20.93At1g70200843356RNA recognition motif (RRM)-containing proteinF:nucleic acid binding;P:unknown;C:chloroplast;MOFBPVAO.I.H.G.S.X.
0.4457.20.92At5g17710831638EMB1241 (embryo defective 1241)F:protein binding, chaperone binding, protein homodimerization activity, adenyl-nucleotide exchange factor activity;P:embryonic development ending in seed dormancy, protein folding;C:thylakoid, chloroplast, chloroplast stroma;BOMFPAVO.I.H.G.S.X.
0.4457.20.91At2g45770819185CPFTSYchloroplast SRP receptor homolog, alpha subunit CPFTSY. Required for LHCP integration into isolated thylakoids.O.I.H.G.S.X.
0.4355.30.92At5g46580834701pentatricopeptide (PPR) repeat-containing proteinF:unknown;P:biological_process unknown;C:chloroplast;POMFBAO.I.H.G.S.X.
0.4355.30.91At5g14460831297pseudouridine 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.
0.4253.90.91At1g21600838761PTAC6 (PLASTID TRANSCRIPTIONALLY ACTIVE6)Present in transcriptionally active plastid chromosomes. Involved in plastid gene expression.O.I.H.G.S.X.
0.4253.90.92At2g25830817125YebC-relatedF:unknown;P:unknown;C:chloroplast;BOFMPO.I.H.G.S.X.
0.4152.40.92At4g02990828116mitochondrial transcription termination factor family protein / mTERF family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMOFBO.I.H.G.S.X.
0.4152.40.92At1g80770844416PDE318 (pigment defective 318)F:GTP binding;P:unknown;C:unknown;BOMFAPO.I.H.G.S.X.
0.3948.40.92At3g53130824479LUT1 (LUTEIN DEFICIENT 1)Lutein-deficient 1 (LUT1) required for lutein biosynthesis, member of the xanthophyll class of carotenoids. Involved in epsilon ring hydroxylation. Maps at 67.3 cM on chromosome 3.O.I.H.G.S.X.
0.3846.70.92At3g07670819958SET domain-containing proteinF:[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity;P:biological_process unknown;C:chloroplast;MFPOO.I.H.G.S.X.
0.3745.00.92At1g74850843824PTAC2 (PLASTID TRANSCRIPTIONALLY ACTIVE2)Present in transcriptionally active plastid chromosomes. Involved in plastid gene expression.O.I.H.G.S.X.
0.3745.00.90At4g00370827908ANTR2Encodes an inorganic phosphate transporter (PHT4;4).O.I.H.G.S.X.
0.3745.00.91At5g16620831524TIC40chloroplast protein import (Tic40)O.I.H.G.S.X.
0.3643.60.91At1g56050842056GTP-binding protein-relatedF:GTP binding;P:biological_process unknown;C:chloroplast, chloroplast stroma;OBMFAPO.I.H.G.S.X.
0.3643.60.90At4g30620829185unknown proteinF:unknown;P:biological_process unknown;C:chloroplast, chloroplast envelope;BOPO.I.H.G.S.X.
0.3541.60.91At3g28460822476unknown proteinF:unknown;P:biological_process unknown;C:chloroplast;BOPAO.I.H.G.S.X.
0.3541.60.92At2g20690816597lumazine-binding family proteinA synthetic gene encoding the catalytic domain of the Arabidopsis thaliana gene At2g20690 was recombinant expressed in E. coli demonstrating the molecular function of riboflavin synthase.O.I.H.G.S.X.
0.3541.60.91At5g48830834941unknown proteinF:molecular_function unknown;P:biological_process unknown;C:chloroplast;BPOO.I.H.G.S.X.
0.3338.10.91At4g20960827843cytidine/deoxycytidylate deaminase family proteinencodes diaminohydroxyphosphoribosylaminopyrimidine deaminase catalyzing the second step in the riboflavin biosynthesisO.I.H.G.S.X.
0.3338.10.91At5g42130834218mitochondrial substrate carrier family proteinF:binding;P:transport, mitochondrial transport;C:mitochondrial inner membrane, chloroplast;MFPOO.I.H.G.S.X.
0.3235.70.91At1g32500840144ATNAP6 (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.
0.3235.70.91At3g58140824983phenylalanyl-tRNA synthetase class IIc family proteinF:in 6 functions;P:tRNA processing, phenylalanyl-tRNA aminoacylation, translation, tRNA aminoacylation for protein translation;C:mitochondrion, chloroplast, membrane;BOMFAPO.I.H.G.S.X.
0.3235.70.91At3g51140824278-F:unknown;P:biological_process unknown;C:chloroplast, chloroplast inner membrane, chloroplast envelope;BPOO.I.H.G.S.X.
0.3133.80.91At3g62910825466APG3 (ALBINO AND PALE GREEN)Isolated in a screen for chloroplast development mutants. Pale green, albino seedlings arrest early in seedling development.O.I.H.G.S.X.
0.3032.10.92At3g10670820236ATNAP7Plastidic SufC-like ATP-binding cassette/ATPase essential for Arabidopsis embryogenesis. Involved in the biogenesis and/or repair of oxidatively damaged FeS clusters. Expressed in embryos and meristems.O.I.H.G.S.X.
0.2930.30.91At5g11480831019GTP bindingF:GTP binding;P:biological_process unknown;C:intracellular, chloroplast;BOFMPAO.I.H.G.S.X.
0.2930.30.92At5g44650834494unknown proteinF:molecular_function unknown;P:biological_process unknown;C:thylakoid, chloroplast thylakoid membrane, chloroplast;PMOO.I.H.G.S.X.
0.2830.30.91At4g15110827177CYP97B3member of CYP97BO.I.H.G.S.X.
0.2726.20.91At5g48220834875indole-3-glycerol phosphate synthase, putativeF:indole-3-glycerol-phosphate synthase activity, catalytic activity;P:metabolic process, tryptophan metabolic process;C:chloroplast, chloroplast stroma;BOAFPO.I.H.G.S.X.
0.2624.40.91At1g02910839350LPA1 (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.
0.2522.60.90At4g36390829791radical 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.
0.2522.60.91At5g08740830775NDC1 (NAD(P)H dehydrogenase C1)F:NADH dehydrogenase activity;P:unknown;C:intrinsic to mitochondrial inner membrane, cell wall, chloroplast, plastoglobule;BOFMAPO.I.H.G.S.X.
0.2420.70.91At1g11430837685plastid developmental protein DAG, putativeF:unknown;P:unknown;C:chloroplast stroma, chloroplast, chloroplast envelope;PO.I.H.G.S.X.
0.2319.30.91At2g41680818766NTRC (NADPH-DEPENDENT THIOREDOXIN REDUCTASE C)Encodes a NADPH thioredoxin reductase involved in chloroplast protection against oxidative damage.O.I.H.G.S.X.
0.2217.50.90At1g11750837719CLPP6One of several nuclear-encoded ClpPs (caseinolytic protease). Contains a 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.
0.2014.40.91At2g42130818813unknown proteinF:unknown;P:biological_process unknown;C:thylakoid, chloroplast, plastoglobule;POO.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
66.299.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
64.599.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
62.699.8GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
54.199.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
49.199.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
40.199.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
30.799.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.699.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
30.699.7GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
29.399.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.799.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.499.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
28.299.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.699.7GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.599.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
27.499.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.499.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
26.599.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.999.7GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.899.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
25.699.7GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
24.599.6GSM152139Col-0 drought 3GSE6583Genome-wide transcriptome analysis of Arabidopsis and siz1-3 response to drought stressLink to GEO
23.899.6GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
23.699.6GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
23.199.6GSM152135Col-0 drought 1GSE6583Genome-wide transcriptome analysis of Arabidopsis and siz1-3 response to drought stressLink to GEO
23.099.6GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
22.899.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.899.6GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
20.399.6GSM133769Lindsey_1-21_torpedo-basal_Rep6_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
19.399.6GSM133756Lindsey_1-10_heart-stage-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
18.299.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
17.999.5GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
14.499.4GSM152137Col-0 drought 2GSE6583Genome-wide transcriptome analysis of Arabidopsis and siz1-3 response to drought stressLink to GEO
14.499.4GSM13780CycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
13.999.4E-ATMX-35-raw-cel-1574334832
12.599.3GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
11.499.3GSM13779Dexamethasone plus cycloheximideGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
10.399.2GSM13784Cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
9.799.1GSM13783Dexamethasone plus cycloheximide - replicateGSE911Identification of LEAFY targets during reproductive transitionLink to GEO
8.699.0GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1023GO: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
0.0912GO:0042793The synthesis of RNA from a plastid DNA template, usually by a specific plastid RNA polymerase.Link to AmiGO
0.0832GO:0045893Any process that activates or increases the frequency, rate or extent of DNA-dependent transcription.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.082200740Riboflavin metabolismLink to KEGG PATHWAY
0.045200970Aminoacyl-tRNA biosynthesisLink to KEGG PATHWAY
0.032100906Carotenoid biosynthesisLink 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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