Co-expression analysis

Gene ID At3g49310
Gene name -
Module size 12 genes
NF 0.25
%ile 27.7



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
1.00100.01.00At3g49310824093-F:unknown;P:unknown;C:endomembrane system;BPMOFAO.I.H.G.S.X.
0.5065.30.90At3g55140824680pectate lyase family proteinF:lyase activity, pectate lyase activity;P:unknown;C:unknown;BPFOO.I.H.G.S.X.
0.4761.20.90At2g25310817069carbohydrate bindingF:carbohydrate binding;P:biological_process unknown;C:endomembrane system;MFPOBO.I.H.G.S.X.
0.4253.90.90At1g15370838106-F:molecular_function unknown;P:transport;C:unknown;POFO.I.H.G.S.X.
0.3846.70.91At2g21600816698ATRER1BKey player of retrieval of ER membrane proteinsO.I.H.G.S.X.
0.3032.10.90At1g75760843909ER lumen protein retaining receptor family proteinF:ER retention sequence binding, receptor activity;P:protein retention in ER lumen, protein transport;C:integral to membrane;MOPFO.I.H.G.S.X.
0.2217.50.90At2g18030816315peptide methionine sulfoxide reductase family proteinF:peptide-methionine-(S)-S-oxide reductase activity, oxidoreductase activity, acting on sulfur group of donors, disulfide as acceptor;P:protein modification process, protein metabolic process;C:endomembrane system;BOMPFAVO.I.H.G.S.X.
0.168.80.90At4g02080827368ATSAR2 (ARABIDOPSIS THALIANA SECRETION-ASSOCIATED RAS SUPER FAMILY 2)A member of ARF-like GTPase family. A thaliana has 21 members, in two subfamilies, ARF and ARF-like (ARL) GTPases.O.I.H.G.S.X.
0.157.80.91At3g48750824036CDC2 (CELL DIVISION CONTROL 2)A-type cyclin-dependent kinase. Together with its specific inhibitor, the Kip-related protein, KRP2 they regulate the mitosis-to-endocycle transition during leaf development. Dominant negative mutations abolish cell division. Loss of function phenotype has reduced fertility with failure to transmit via pollen. Pollen development is arrested at the second mitotic division. Expression is regulated by environmental and chemical signals. Part of the promoter is responsible for expression in trichomes. Functions as a positive regulator of cell proliferation during development of the male gametophyte, embryo and endosperm. Phosphorylation of threonine 161 is required for activation of its associated kinase.O.I.H.G.S.X.
0.157.80.90At3g54300824597ATVAMP727 (VESICLE-ASSOCIATED MEMBRANE PROTEIN 727)Encodes a member of Synaptobrevin -like protein family. VAMP727 is a R-SNARE and interacts with SYP22/VTI11/SYP51. It is required for trafficking of storage proteins to the protein storage vacuoles (PSV) and also for PSV organization and biogenesis. Loss of function mutations have no phenotype but double mutants with SYP22 are embryo lethal.O.I.H.G.S.X.
0.146.80.90At3g05280819692integral membrane Yip1 family proteinF:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MOFPO.I.H.G.S.X.
0.082.30.90At2g43070818909protease-associated (PA) domain-containing proteinF:peptidase activity, aspartic-type endopeptidase activity;P:proteolysis;C:plasma membrane;MPOBFAO.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
144.299.9GSM205430met1-3_leaf_fourth-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
121.899.9GSM205435Col_ leaf_ wildtype_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
100.799.9GSM205432Col_ leaf_ wildtype_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
77.099.9GSM205428met1-3_leaf_fourth-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
64.699.8GSM184556Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
55.899.8GSM143308Tsu_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
54.199.8GSM253651Ler 1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
53.899.8GSM205426met1-3_leaf_second-selfed generation_rep02GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
53.899.8GSM253652Ler 2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
53.499.8GSM143307Low_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
51.899.8GSM205364met1-3_leaf_second-selfed generation_rep01GSE8279Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG MethylationLink to GEO
50.199.8GSM143310Tsu_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.199.8GSM143309Tsu_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
49.099.8GSM253650Ler 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
47.799.8GSM253645High_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
44.899.8GSM133303RIKEN-NAKABAYASHI1AGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
43.899.8GSM253646Low_Mo_seg_pool_Ler_col_F2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
41.599.8GSM143299High_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
40.599.8GSM143302Ts_genomic_hyb_1GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
37.799.7GSM143306High_Na_seg_pool_tsu_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.899.7GSM143301Ts_genomic_hyb_2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
35.699.7GSM133304RIKEN-NAKABAYASHI1BGSE5700AtGenExpress: Effect of ABA during seed imbibitionLink to GEO
34.799.7GSM253648Col-0-1GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
33.599.7GSM226530LCOLUMELLASBGSE8934A high resolution organ expression map reveals novel expression patterns and predicts cellular functionLink to GEO
33.599.7GSM143298Low_Na_seg_pool_ts_col_F2GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
31.999.7GSM253647Col-0 3GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
31.699.7GSM253649Col-0-2GSE10039Low_Mo_Arabidopsis_mapping_MOT1Link to GEO
30.499.7E-MEXP-849-raw-cel-1181980990
29.799.7GSM143300Ts_genomic_hyb_3GSE6203Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1Link to GEO
27.299.7E-MEXP-849-raw-cel-1181980982
23.499.6GSM131706ATGE_84_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
21.299.6GSM131707ATGE_84_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
19.599.6GSM184537Whole roots 2hr KCl control treated then frozen, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
18.999.5GSM131703ATGE_83_AGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
18.899.5E-MEXP-849-raw-cel-1181980998
18.799.5GSM131705ATGE_83_CGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
18.199.5GSM131708ATGE_84_DGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
16.999.5GSM131704ATGE_83_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
15.699.5GSM133314RIKEN-LI2BGSE5701AtGenExpress: Basic hormone treatment of seedsLink to GEO
15.699.5GSM133120RIKEN-YAMAUCHI2BGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
15.399.4GSM133312RIKEN-LI1BGSE5701AtGenExpress: Basic hormone treatment of seedsLink to GEO
15.099.4GSM184551Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
14.799.4E-ATMX-35-raw-cel-1574334864
14.499.4E-ATMX-35-raw-cel-1574334880
14.399.4GSM142740DH001_ATH1_A7-MPG1GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
13.799.4GSM133117RIKEN-YAMAUCHI1AGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
13.499.4GSM133318RIKEN-LI4BGSE5701AtGenExpress: Basic hormone treatment of seedsLink to GEO
12.899.3GSM133119RIKEN-YAMAUCHI2AGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
12.499.3GSM133762Lindsey_1-14_torpedo-root_Rep1_ATH1GSE5730Transcriptional profiling of laser-capture micro-dissected embryonic tissuesLink to GEO
11.499.3GSM133118RIKEN-YAMAUCHI1BGSE5687AtGenExpress: Different temperature treatment of seedsLink to GEO
11.399.3GSM239251Columbia glabrous (C24) wild type pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
11.399.3E-MEXP-1138-raw-cel-1432772938
11.399.3E-MEXP-1138-raw-cel-1432772970
10.699.2GSM154503Arabidopsis desiccated mature pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
10.699.2E-MEXP-1138-raw-cel-1432772906
10.699.2GSM133966Fukuda_1-11_10A_Rep1_ATH1GSE5748In vitro tracheary element transdifferentiation of Col-0 suspension cells.Link to GEO
10.599.2GSM131701ATGE_82_BGSE5634AtGenExpress: Developmental series (siliques and seeds)Link to GEO
10.299.2E-MEXP-285-raw-cel-440782791
10.099.2E-MEXP-285-raw-cel-440782725
9.999.1GSM184497Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1GSE7631Cell-specific nitrogen responses in the Arabidopsis rootLink to GEO
9.899.1GSM142739DH001_ATH1_A6-TCP2GSE6162Transcriptome analysis of Arabidopsis microgametogenesisLink to GEO
9.799.1E-MEXP-1138-raw-cel-1432772714
9.699.1GSM154506Arabidopsis hydrated pollen grains rep2GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
9.599.1GSM131637ATGE_73_BGSE5632AtGenExpress: Developmental series (flowers and pollen)Link to GEO
9.199.1E-MEXP-1138-raw-cel-1432772778
9.099.1E-MEXP-1138-raw-cel-1432773002
9.099.1GSM154505Arabidopsis hydrated pollen grains rep1GSE6696Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in ArabidopsisLink to GEO
9.099.1E-MEXP-98-raw-cel-320188749
8.999.0E-ATMX-35-raw-cel-1574334848
8.999.0GSM133313RIKEN-LI2AGSE5701AtGenExpress: Basic hormone treatment of seedsLink to GEO
8.999.0GSM239253CaMV::DME pollenGSE9408Identification of putative Arabidopsis DEMETER target genes by GeneChip AnalysisLink to GEO
8.999.0E-MEXP-1138-raw-cel-1432772842
8.699.0E-MEXP-1138-raw-cel-1432773130

Biological processes inferred to relate to the module

SFGenesGO IDProcess NameLink to AmiGO
0.1251GO:0048229The process whose specific outcome is the progression of the gametophyte over time, from its formation to the mature structure. The gametophyte is the gamete-producing individual or phase in the life cycle having alternation of generations. An example of this process is found in Arabidopsis thaliana.Link to AmiGO
0.1111GO:0006621The retention in the endoplasmic reticulum (ER) lumen of soluble resident proteins. Sorting receptors retrieve proteins with ER localization signals, such as KDEL and HDEL sequences or some transmembrane domains, that have escaped to the cis-Golgi network and return them to the ER. Abnormally folded proteins and unassembled subunits are also selectively retained in the ER.Link to AmiGO
0.1111GO:0006890The directed movement of substances from the Golgi back to the endoplasmic reticulum, mediated by vesicles bearing specific protein coats such as COPI or COG.Link to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG
0.045100040Pentose and glucuronate interconversionsLink 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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