Co-expression analysis

Gene ID At5g06140
Gene name SNX1 (SORTING NEXIN 1)
Module size 7 genes
NF 0.31
%ile 38.4



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
0.3338.11.00At5g06140830501SNX1 (SORTING NEXIN 1)Homolog of yeast retromer subunit VPS5. Part of a retromer-like protein complex involved in endosome to lysosome protein transport. In roots it co-localizes with the PIN2 auxin efflux carrier. Involved in endocytic sorting of membrane proteins including PIN2, BOR1 and BRI1.O.I.H.G.S.X.
0.6075.70.93At4g21450826300vesicle-associated membrane family protein / VAMP family proteinF:structural molecule activity;P:biological_process unknown;C:plasma membrane;MOFPBVO.I.H.G.S.X.
0.5065.30.93At3g25910822188zinc ion bindingF:zinc ion binding;P:biological_process unknown;C:intracellular;MPOFBVO.I.H.G.S.X.
0.2930.30.93At2g29400817489TOPP1 (TYPE ONE PROTEIN PHOSPHATASE 1)Type 1 protein phosphatase, expressed in roots, rosettes and flowersO.I.H.G.S.X.
0.2930.30.93At5g13570831201DCP2 (DECAPPING 2)Encodes DCP2 with mRNA decapping activity. DCP2 forms a mRNA decapping complex with DCP1 (At1g08370) and VCS (VARICOSE) (At3g13300). Recombinant DCP2 is enzymatically active in vitro, generating from capped mRNAs m7GDP, and 5-phosphorylated mRNAs. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. The protein was shown by immunoprecipitation not to interact with DCP1.O.I.H.G.S.X.
0.2014.40.93At4g39910830150ATUBP3 (ARABIDOPSIS THALIANA UBIQUITIN-SPECIFIC PROTEASE 3)Encodes a nuclear ubiquitin-specific protease.O.I.H.G.S.X.
0.1710.20.93At2g21240816663BPC4 (BASIC PENTACYSTEINE 4)F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:nucleus;PMBO.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
99.599.9GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
98.699.9GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
98.599.9GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
88.499.9GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
88.199.9GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
87.099.9GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
84.599.9GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
81.899.9GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
79.499.9GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
77.499.9GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
76.999.9GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
76.499.9GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
72.399.9GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
70.999.9GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
68.699.9GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
64.099.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
61.499.8GSM133754Turner_A-8-Turne-WT-Base2_SLDGSE5729Role of COV in vascular patterningLink to GEO
59.799.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
55.799.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
44.499.8GSM133753Turner_A-7-Turne-WT-Base1_SLDGSE5729Role of COV in vascular patterningLink to GEO
38.999.8GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
27.099.7E-MEXP-791-raw-cel-1122937569
26.599.7GSM131065Hammond_2-6_pho1mutant_Rep3_ATH1GSE5611Differential gene expression patterns in the phosphate deficient mutant, pho 1Link to GEO
26.299.7GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
24.799.6GSM133957Fukuda_1-2_0B_Rep2_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
24.799.6GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
22.399.6E-MEXP-791-raw-cel-1122937533
21.899.6E-MEXP-509-raw-cel-829148090
21.299.6E-MEXP-509-raw-cel-829148597
19.699.6GSM131063Hammond_2-4_pho1mutant_Rep2_ATH1GSE5611Differential gene expression patterns in the phosphate deficient mutant, pho 1Link to GEO
19.599.6E-MEXP-509-raw-cel-829148772
17.399.5GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
16.899.5E-MEXP-509-raw-cel-829148165
16.799.5GSM133866Cain_1-1_WT1_Rep1_ATH1GSE5740Polycomb Binding ProteinLink to GEO
15.699.5GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
15.499.5E-MEXP-509-raw-cel-829148913
15.099.4GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.199.4GSM133868Cain_1-2_WT1_Rep2_ATH1GSE5740Polycomb Binding ProteinLink to GEO
13.799.4GSM131655ATGE_27_AGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
13.499.4E-MEXP-1451-raw-cel-1585200362
13.499.4GSM133869Cain_1-4_CDB1-Knockout_Rep2_ATH1GSE5740Polycomb Binding ProteinLink to GEO
12.599.3GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
11.899.3E-MEXP-791-raw-cel-1122937551
11.499.3GSM131657ATGE_27_CGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
10.899.2GSM133867Cain_1-3_CDB1-Knockout_Rep1_ATH1GSE5740Polycomb Binding ProteinLink to GEO
10.499.2GSM131061Hammond_2-2_pho1mutant_Rep1_ATH1GSE5611Differential gene expression patterns in the phosphate deficient mutant, pho 1Link to GEO
10.399.2GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
10.399.2E-MEXP-509-raw-cel-829148561
10.199.2GSM270866Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep1GSE10719Response of Arabidopsis cell culture to phytoprostane A1Link to GEO
10.099.2E-MEXP-791-raw-cel-1122937605
9.699.1GSM226538L8SBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
9.399.1GSM131656ATGE_27_BGSE5633AtGenExpress: Developmental series (shoots and stems)Link to GEO
9.299.1GSM226535L5SBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
9.299.1GSM142637MC002_ATH1_A5.3-dubos-5kxGSE6151The mechanisms involved in the interplay between dormancy and secondary growth in ArabidopsisLink to GEO
9.199.1E-ATMX-33-raw-cel-1562596197
8.799.0GSM184907Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 1GSE7641Expression analysis of root cell-types after treatment with saltLink to GEO
8.799.0GSM128706Shirras_3-3_LabCalcicole-12.5mM-CaCl2_Rep1_ATH1GSE5523Environmental Genomics of Calcicole-calcifuge physiologyLink to GEO

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.2001GO:0006402The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.Link to AmiGO
0.1821GO:0008333The directed movement of substances from endosomes to lysosomes.Link to AmiGO
0.1821GO:0031087Cleavage of the 5'-cap of a nuclear-transcribed mRNA that is independent of poly(A) tail shortening.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.036103018RNA degradationLink 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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