Co-expression analysis

Gene ID At1g23820
Gene name SPDS1 (spermidine synthase 1)
Module size 7 genes
NF 0.15
%ile 11.3



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
1.00100.01.00At1g23820838993SPDS1 (spermidine synthase 1)Spermidine synthase.O.I.H.G.S.X.
0.2930.30.91At2g39990818587EIF2translation initiation factor eIF2 p47 subunit homologO.I.H.G.S.X.
0.2522.60.91At1g4883084130540S ribosomal protein S7 (RPS7A)F:structural constituent of ribosome;P:translation;C:cytosolic small ribosomal subunit, cytosolic ribosome, cell wall, plasma membrane, chloroplast;MPOFO.I.H.G.S.X.
0.2522.60.91At3g57290824896EIF3E (EUKARYOTIC TRANSLATION INITIATION FACTOR 3E)Encodes a protein that is found in not only the eif3 complex but also in association with subunits of the COP9 signalosome. eIF3e appears to be subjected to proteasome-dependent degradation that requires the PCI domain of eIF3e. The level of eIF3e present in cells appears to affect the rate of translation.O.I.H.G.S.X.
0.2014.40.91At5g3553083351840S ribosomal protein S3 (RPS3C)F:structural constituent of ribosome;P:response to salt stress, translation;C:cytosolic small ribosomal subunit, cytosolic ribosome, nucleolus, membrane;BOMAPFO.I.H.G.S.X.
0.082.30.91At3g0920082007660S acidic ribosomal protein P0 (RPP0B)F:structural constituent of ribosome;P:translational elongation, response to salt stress, response to cold, translation;C:in 7 components;MOAFPBO.I.H.G.S.X.
0.061.40.91At3g14290820649PAE2Encodes 20S proteasome subunit PAE2 (PAE2).O.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
119.799.9GSM284394Arabidopsis GCE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
114.499.9GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
79.699.9GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
73.999.9GSM284392Arabidopsis GCE1GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
68.399.9GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
64.099.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
61.199.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
61.199.8GSM311280Laser 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
59.399.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
58.899.8GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
57.399.8GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
53.299.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
52.399.8GSM284393Arabidopsis GCE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
49.799.8GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.599.8GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
45.299.8GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.799.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
43.199.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.299.8GSM311279Laser 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
40.099.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.099.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
36.599.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.899.7GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
34.299.7GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
34.099.7GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
32.199.7GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.799.7GSM154508Arabidopsis growing pollen tubes rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
26.599.7E-MEXP-285-raw-cel-440782725
26.099.7GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
26.099.7E-ATMX-35-raw-cel-1574334864
25.599.7E-MEXP-285-raw-cel-440782791
25.599.7GSM311278Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
23.899.6E-ATMX-35-raw-cel-1574334880
22.299.6GSM154506Arabidopsis hydrated pollen grains rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
21.299.6E-ATMX-35-raw-cel-1574334848
19.899.6GSM239251Columbia glabrous (C24) wild type pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
19.599.6GSM154504Arabidopsis desiccated mature pollen grains rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
19.499.6GSM311277Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 1GSE12402Expression data from Arabidopsis seed compartments at the pre-globular stageLink to GEO
19.499.6E-MEXP-1138-raw-cel-1432772970
19.499.6GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
18.999.5GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
18.799.5E-MEXP-1138-raw-cel-1432772522
18.499.5GSM131638ATGE_73_CGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
18.199.5E-MEXP-1138-raw-cel-1432773098
17.799.5GSM239253CaMV::DME pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
17.699.5E-MEXP-1138-raw-cel-1432773002
17.399.5E-MEXP-1138-raw-cel-1432773130
16.999.5GSM131636ATGE_73_AGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
16.799.5E-MEXP-1138-raw-cel-1432772586
16.499.5GSM284390Arabidopsis GPE2GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
16.499.5E-MEXP-1138-raw-cel-1432772682
16.399.5E-MEXP-1138-raw-cel-1432772554
16.199.5E-MEXP-1138-raw-cel-1432772714
16.099.5GSM311292Laser 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
15.999.5GSM131637ATGE_73_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
15.599.5E-MEXP-1138-raw-cel-1432773226
15.499.5GSM154507Arabidopsis growing pollen tubes rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
15.199.4GSM154505Arabidopsis hydrated pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
15.199.4E-MEXP-1138-raw-cel-1432772842
15.099.4E-MEXP-1138-raw-cel-1432772906
14.999.4E-MEXP-1138-raw-cel-1432772650
14.899.4E-MEXP-1138-raw-cel-1432772618
14.599.4GSM284391Arabidopsis GPE3GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
14.599.4E-MEXP-1138-raw-cel-1432773194
14.099.4E-MEXP-1138-raw-cel-1432772810
13.399.4GSM284385Arabidopsis GEP6GSE11262Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.Link to GEO
13.299.4E-MEXP-1138-raw-cel-1432772938
13.299.4GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
13.199.4E-MEXP-807-raw-cel-1173273170
12.999.3GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
12.699.3E-MEXP-1138-raw-cel-1432773162
12.599.3E-MEXP-1138-raw-cel-1432772874
12.599.3GSM133766Lindsey_1-18_torpedo-root_Rep3_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
12.499.3E-MEXP-1138-raw-cel-1432772746
12.399.3GSM239254CaMV::DME stamenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
12.199.3E-MEXP-807-raw-cel-1173273196
11.999.3GSM239252Columbia glabrous (C24) wild type stamenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
11.599.3GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
11.399.3GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.999.2E-MEXP-1138-raw-cel-1432772778
10.599.2E-MEXP-1138-raw-cel-1432773354
9.999.1E-MEXP-1138-raw-cel-1432773386

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1671GO:0008295The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.Link to AmiGO
0.0491GO:0006352Any process involved in the assembly of the RNA polymerase complex at the promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter.Link to AmiGO
0.0431GO:0009640The control of plant growth, development, and differentiation by the duration and nature of light, independent of photosynthesis.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.083100410beta-Alanine metabolismLink to KEGG PATHWAY
0.035100330Arginine and proline metabolismLink to KEGG PATHWAY
0.033100480Glutathione 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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