Co-expression analysis

Gene ID At5g53120
Gene name SPDS3 (SPERMIDINE SYNTHASE 3)
Module size 20 genes
NF 0.11
%ile 7.7



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
1.00100.01.00At5g53120835392SPDS3 (SPERMIDINE SYNTHASE 3)encodes a novel spermine synthase and is a paralog of previously characterized spermidine synthases, SPDS1 and SPDS2. SPDS3 forms heterodimers with SDPS2, which in turn forms heterodimers with SDPS1 in vivo. The gene does not complement speDelta3 deficiency of spermidine synthase in yeast but DOES complement speDelta4 deficiency.O.I.H.G.S.X.
0.2830.30.82At2g04350814974long-chain-fatty-acid--CoA ligase family protein / long-chain acyl-CoA synthetase family protein (LACS8)F:long-chain-fatty-acid-CoA ligase activity, catalytic activity;P:fatty acid biosynthetic process, metabolic process;C:endoplasmic reticulum;BOMFPAVO.I.H.G.S.X.
0.2522.60.78At2g23080816838casein kinase II alpha chain, putativeF:protein serine/threonine kinase activity, protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:cellular_component unknown;MOPFBVAO.I.H.G.S.X.
0.2115.80.78At5g40930834094TOM20-4 (TRANSLOCASE OF OUTER MEMBRANE 20-4)Form of TOM20, which is a component of the TOM complex involved in transport of nuclear-encoded mitochondrial proteinsO.I.H.G.S.X.
0.2115.80.80At2g43020818904ATPAO2 (Polyamine oxidase 2)F:electron carrier activity, amine oxidase activity, oxidoreductase activity;P:unknown;C:cellular_component unknown;BMOPFAO.I.H.G.S.X.
0.146.80.79At5g04410830320NAC2NAC family member, hypothetical transcriptional regulatorO.I.H.G.S.X.
0.135.80.79At2g21270816666ubiquitin fusion degradation UFD1 family proteinF:molecular_function unknown;P:ubiquitin-dependent protein catabolic process;C:unknown;OFMPABO.I.H.G.S.X.
0.124.90.78At1g49710841394FUT12 (FUCOSYLTRANSFERASE 12)Encodes a protein with core α1,3-fucosyltransferase activity.O.I.H.G.S.X.
0.124.90.78At3g61710825344autophagy protein Apg6 familyF:molecular_function unknown;P:autophagy;C:unknown;MOFBPVAO.I.H.G.S.X.
0.124.90.78At5g59210836039myosin heavy chain-relatedF:unknown;P:biological_process unknown;C:unknown;MOBFPAVO.I.H.G.S.X.
0.114.10.78At4g07390826170PQ-loop repeat family protein / transmembrane family proteinF:unknown;P:unknown;C:membrane;MPFOO.I.H.G.S.X.
0.114.10.78At5g64500836571membrane protein-relatedF:molecular_function unknown;P:biological_process unknown;C:membrane;BOFMAPO.I.H.G.S.X.
0.103.40.78At1g27530839644-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOPO.I.H.G.S.X.
0.103.40.78At1g28120839705-F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPO.I.H.G.S.X.
0.082.30.78At3g19640821501magnesium transporter CorA-like family protein (MRS2-3)F:metal ion transmembrane transporter activity;P:metal ion transport;C:plasma membrane, membrane;PFMOBO.I.H.G.S.X.
0.082.30.78At3g04240819579SEC (secret agent)Has O-linked N-acetyl glucosamine transferase activity. Similar to Arabidopsis SPY gene.O.I.H.G.S.X.
0.071.90.78At4g11800826786hydrolase/ protein serine/threonine phosphataseF:hydrolase activity, protein serine/threonine phosphatase activity;P:biological_process unknown;C:endoplasmic reticulum;BPOO.I.H.G.S.X.
0.061.40.77At3g62580825432-F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MFPBO.I.H.G.S.X.
0.051.10.78At4g23630828463BTI1 (VIRB2-INTERACTING PROTEIN 1)F:unknown;P:biological_process unknown;C:endoplasmic reticulum, plasma membrane, vacuole;MPOFO.I.H.G.S.X.
0.040.90.77At5g35180833472phosphoinositide bindingF:phosphoinositide binding;P:signal transduction;C:plasma membrane;POMFVO.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
140.199.9GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
103.999.9GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
98.199.9GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
82.199.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
73.699.9GSM311280Laser 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
60.699.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
57.999.8GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
57.899.8GSM311279Laser 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
56.999.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
52.199.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
51.399.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
50.799.8GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.099.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.099.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
46.899.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
46.699.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
45.899.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.999.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.499.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.399.8GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
41.899.8GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
40.099.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
37.799.7GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.599.7GSM311292Laser 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
37.499.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.799.7GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.599.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
33.799.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.399.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
32.299.7GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
29.199.7GSM311291Laser 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
28.599.7GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.799.6GSM311293Laser 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
20.399.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
19.899.6GSM142631MC002_ATH1_A3.3-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
19.199.6GSM142624MC002_ATH1_A1.2-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
18.899.5GSM311294Laser 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
17.499.5GSM142623MC002_ATH1_A1.1-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
16.999.5GSM142629MC002_ATH1_A3.1-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
16.799.5E-MEXP-285-raw-cel-440782725
16.799.5GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
16.099.5GSM142625MC002_ATH1_A1.3-dubos-wtxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
14.399.4GSM239251Columbia glabrous (C24) wild type pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
14.399.4E-MEXP-285-raw-cel-440782791
13.699.4GSM239253CaMV::DME pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
13.599.4E-ATMX-35-raw-cel-1574334864
12.099.3GSM142630MC002_ATH1_A3.2-dubos-6kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
12.099.3E-ATMX-35-raw-cel-1574334880
11.799.3GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.699.3GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
10.599.2GSM131637ATGE_73_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.899.1GSM131638ATGE_73_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.799.1E-ATMX-35-raw-cel-1574334848
9.699.1GSM133774Lindsey_1-26_torpedo-meristem_Rep2_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
9.599.1GSM176876AWP_AL_Txed_1GSE7334Microarray Analysis of Arabidopsis Genome Response to Aluminum StressLink to GEO
9.499.1GSM131636ATGE_73_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.499.1GSM142636MC002_ATH1_A5.2-dubos-5kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.299.1GSM142634MC002_ATH1_A4.3-dubos-6kcGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.299.1GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
8.799.0GSM142633MC002_ATH1_A4.2-dubos-6kcGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.0951GO:0006493The formation of O-glycans by addition of glycosyl groups either to the hydroxyl group of peptidyl-serine, peptidyl-threonine, peptidyl-hydroxylysine, or peptidyl-hydroxyproline, or to the phenol group of peptidyl-tyrosine.Link to AmiGO
0.0831GO:0006596The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.Link to AmiGO
0.0561GO: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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.054100410beta-Alanine metabolismLink to KEGG PATHWAY
0.041104712Circadian rhythm - plantLink to KEGG PATHWAY
0.029100330Arginine and proline 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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