Co-expression analysis

Gene ID At5g07470
Gene name PMSR3 (PEPTIDEMETHIONINE SULFOXIDE REDUCTASE 3)
Module size 18 genes
NF 0.25
%ile 27.2



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
1.00100.01.00At5g07470830638PMSR3 (PEPTIDEMETHIONINE SULFOXIDE REDUCTASE 3)ubiquitous enzyme that repairs oxidatively damaged proteinsO.I.H.G.S.X.
0.5065.30.91At1g54320841873LEM3 (ligand-effect modulator 3) family protein / CDC50 family proteinF:unknown;P:biological_process unknown;C:chloroplast, membrane;MOFPO.I.H.G.S.X.
0.3846.70.91At4g15940827276fumarylacetoacetate hydrolase family proteinF:catalytic activity;P:metabolic process;C:mitochondrion;BOFMAPO.I.H.G.S.X.
0.3541.60.91At4g15470827218-F:unknown;P:unknown;C:unknown;BOMPFVO.I.H.G.S.X.
0.3338.10.93At1g03900839378ATNAP4 (Arabidopsis thaliana non-intrinsic ABC protein 4)member of NAP family, an heterogeneous subfamily of the ATP-binding Cassette (ABC) superfamily of membrane transporters. The NAPs proteins are characterized by having only one nucleotide-binding folds (NBFs) domain.O.I.H.G.S.X.
0.3338.10.91At3g04090819564SIP1A (SMALL AND BASIC INTRINSIC PROTEIN 1A)Belongs to a family of plant aquaporins. Similar to yeast and radish aquaporins. Located on ER.O.I.H.G.S.X.
0.3235.70.91At3g19950821533zinc finger (C3HC4-type RING finger) family proteinF:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFVBO.I.H.G.S.X.
0.2726.20.91At1g11910837740aspartyl protease family proteinF:aspartic-type endopeptidase activity;P:proteolysis, response to salt stress;C:vacuole;MFOPBO.I.H.G.S.X.
0.2624.40.92At1g16180838187TMS membrane family protein / tumour differentially expressed (TDE) family proteinF:molecular_function unknown;P:unknown;C:endomembrane system, membrane;MFPOO.I.H.G.S.X.
0.2420.70.91At3g46060823749ATRAB8Asmall GTP-binding protein (ara-3)O.I.H.G.S.X.
0.2217.50.92At1g32790840173RNA-binding protein, putativeRNA-binding protein, putative, similar to RNA-binding protein GB:CAB40027 GI:4539439 from (Arabidopsis thaliana).Member of a family of PAB2 binding domain proteins.O.I.H.G.S.X.
0.2217.50.91At1g16240838193SYP51 (SYNTAXIN OF PLANTS 51)Encodes one of 24 Arabidopsis syntaxins. Its mRNA has been shown to be expressed.O.I.H.G.S.X.
0.1710.20.91At5g58060835918YKT61member of YKT6 Gene FamilyO.I.H.G.S.X.
0.1710.20.92At5g58740835988nuclear movement family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPFO.I.H.G.S.X.
0.1710.20.91At5g11770831049NADH-ubiquinone oxidoreductase 20 kDa subunit, mitochondrialF:4 iron, 4 sulfur cluster binding, NADH dehydrogenase (ubiquinone) activity, oxidoreductase activity, acting on NADH or NADPH;P:mitochondrial electron transport, NADH to ubiquinone;C:mitochondrion, respiratory chain complex I;BOPAMFO.I.H.G.S.X.
0.124.90.91At1g71190843459SAG18 (SENESCENCE ASSOCIATED GENE 18)Senescence associated gene (SAG). Expression induced by ozone. Encodes a plant-specific protein of unknown function. Based on a personal communication from David Meinke (08/21/2007), this gene is not allelic to TTN4, even though this has been stated previously in a publication.O.I.H.G.S.X.
0.114.10.91At5g06260830513nucleolar protein-relatedF:calcium ion binding;P:N-terminal protein myristoylation;C:cellular_component unknown;MOPFO.I.H.G.S.X.
0.092.80.92At1g27530839644-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPO.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
74.899.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
69.099.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
67.499.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
42.999.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
34.299.7GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
33.399.7GSM284397Arabidopsis GGSc1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
32.299.7GSM284398Arabidopsis GGSc2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
30.999.7GSM133757Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
28.199.7E-ATMX-35-raw-cel-1574334832
27.899.7E-MEXP-1443-raw-cel-1581869515
24.799.6E-MEXP-828-raw-cel-1156922944
23.799.6E-MEXP-509-raw-cel-829148703
23.399.6GSM311284Laser capture microdissected (LCM) general seed coat at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
22.399.6GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
22.199.6GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
20.099.6GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
19.999.6GSM311285Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
19.899.6GSM311283Laser capture microdissected (LCM) general seed coat at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
19.299.6GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
19.099.5GSM311286Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
18.499.5E-MEXP-1443-raw-cel-1581869573
18.199.5GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
17.799.5GSM131449AtGen_6-9221_Heatstress-Roots-1.0h_Rep1GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
17.699.5GSM311291Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
16.799.5E-MEXP-828-raw-cel-1156922684
16.599.5GSM131450AtGen_6-9222_Heatstress-Roots-1.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
15.899.5GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
15.799.5GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
15.699.5GSM147965lec1-1 Globular Stage Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
15.599.5GSM10480lec1-1 Cotyledon Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
15.499.5GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.699.4GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.499.4GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
14.399.4GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
14.299.4E-ATMX-35-raw-cel-1574334800
14.199.4GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
13.899.4E-ATMX-35-raw-cel-1574334816
13.799.4GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
13.799.4GSM39200Col_C2GSE2169rre1 and rre2 mutantsLink to GEO
13.699.4GSM10479lec1-1 Cotyledon Stage Seed 1GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
13.599.4E-MEXP-828-raw-cel-1156922846
12.799.3GSM147966lec1-1 Globular Stage Seed 2GSE1051Seed development in LEAFY COTYLEDON1 mutantsLink to GEO
11.699.3GSM10448WT Cotyledon Stage Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
11.299.2GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
10.999.2GSM133761Lindsey_1-13_torpedo-cotyledon_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
10.799.2GSM147964WT Globular Stage Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
10.799.2GSM10449WT Cotyledon Stage Seed 2GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO
10.799.2E-MEXP-828-raw-cel-1156922923
10.199.2GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
10.099.2GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
10.099.2GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
9.999.1GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
9.599.1GSM311292Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2GSE12403Expression data from Arabidopsis seed compartments at the linear-cotyledon stageLink to GEO
9.499.1GSM131448AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2GSE5628AtGenExpress: Stress Treatments (Heat stress)Link to GEO
9.099.1GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
8.999.0GSM147963WT Globular Stage Seed 1GSE680Transcript Profiling of Arabidopsis Plant Life CycleLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1051GO:0006858The transport of substances that occurs outside cells.Link to AmiGO
0.0771GO:0006120The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex I.Link to AmiGO
0.0771GO:0010149A preprogrammed process associated with the dismantling of an anatomical structure and an overall decline in metabolism. This may include the breakdown of organelles, membranes and other cellular components. An example of this process is found in Arabidopsis thaliana, when older leaves or floral organs are shed.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.061204130SNARE interactions in vesicular transportLink to KEGG PATHWAY
0.013100190Oxidative phosphorylationLink to KEGG PATHWAY
0.002101100Metabolic pathwaysLink 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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