Co-expression analysis

Gene ID	At1g08190
Gene name	vacuolar assembly protein, putative (VPS41)
Module size	5 genes
NF	0.10
%ile	6.5

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : 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
1.00	100.0	1.00	At1g08190	837340	vacuolar assembly protein, putative (VPS41)	F:protein binding, binding, nucleotide binding, zinc ion binding;P:intracellular protein transport, vesicle-mediated transport;C:unknown;MOFPVBA	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.33	38.1	0.91	At4g13020	826915	MHK	Encodes a member of the cdc2+ family of protein kinases MHK. Similar to the mak genes of rats. mak encodes a protein kinase that may play a role in spermatogenesis.	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.32	35.7	0.92	At4g39080	830063	VHA-A3 (VACUOLAR PROTON ATPASE A3)	Vacuolar proton ATPase subunit VHA-a isoform 3. Localized in the tonoplast.	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.12	4.9	0.92	At3g08930	820042	-	F:unknown;P:unknown;C:endomembrane system;MOFP	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)
0.03	0.6	0.92	At4g36630	829815	EMB2754 (EMBRYO DEFECTIVE 2754)	F:small GTPase regulator activity, binding;P:embryonic development ending in seed dormancy;C:cellular_component unknown;MFOP	O.I.	H.G.	S.X.	Please selectTAIR (integral)KEGG (integral)PlantTribes (integral)Gramene (integral)MPSS (genome)InParanoid (ortholog)Plant RBP (ortholog)SIGnAL (T-DNA)RAFL (full-length clone)AtGDB (genome)Genevestigator (expression)eFP Browser (expression)AVT (expression)ATTED-II (co-expression)AtcisDB (cis-element)SUBA (hydropathy)AtProteomePlant Proteome DatabasePMN (pathway)KaPPA-View 4 (pathway)RnR (over-expression)iHOP (report)

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
74.7	99.9	E-MEXP-807-raw-cel-1173273170
48.5	99.8	E-MEXP-807-raw-cel-1173273223
46.8	99.8	GSM154507	Arabidopsis growing pollen tubes rep1	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
45.8	99.8	E-MEXP-807-raw-cel-1173272948
43.2	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
39.9	99.8	GSM154503	Arabidopsis desiccated mature pollen grains rep1	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
35.7	99.7	E-MEXP-807-raw-cel-1173273252
34.2	99.7	GSM154505	Arabidopsis hydrated pollen grains rep1	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
32.4	99.7	E-MEXP-1138-raw-cel-1432772938
30.9	99.7	E-MEXP-1138-raw-cel-1432772906
30.3	99.7	E-MEXP-1138-raw-cel-1432772810
28.7	99.7	GSM142851	MG001_ATH1_A4-Torres-2N1	GSE6176	Impact of Type III effectors on plant defense responses
28.1	99.7	E-MEXP-1138-raw-cel-1432772874
27.5	99.7	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
27.1	99.7	E-MEXP-1138-raw-cel-1432772842
26.7	99.7	E-MEXP-807-raw-cel-1173273116
26.3	99.7	E-MEXP-1138-raw-cel-1432772746
26.2	99.7	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
26.2	99.7	E-MEXP-1138-raw-cel-1432772778
25.8	99.7	E-MEXP-1138-raw-cel-1432772682
25.6	99.7	E-MEXP-1138-raw-cel-1432772618
25.0	99.6	E-MEXP-1138-raw-cel-1432772650
24.9	99.6	E-MEXP-1138-raw-cel-1432772586
24.6	99.6	E-MEXP-807-raw-cel-1173273060
24.5	99.6	E-MEXP-1138-raw-cel-1432772522
24.2	99.6	E-MEXP-1138-raw-cel-1432772714
24.1	99.6	E-MEXP-1138-raw-cel-1432772554
23.7	99.6	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
22.8	99.6	GSM154504	Arabidopsis desiccated mature pollen grains rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
22.7	99.6	GSM154508	Arabidopsis growing pollen tubes rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
22.6	99.6	E-MEXP-1138-raw-cel-1432773066
22.5	99.6	GSM184551	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
22.4	99.6	E-MEXP-1138-raw-cel-1432773322
21.2	99.6	E-MEXP-1138-raw-cel-1432773098
21.0	99.6	E-MEXP-1138-raw-cel-1432773194
20.8	99.6	E-MEXP-1138-raw-cel-1432773034
20.5	99.6	E-MEXP-1138-raw-cel-1432773258
20.2	99.6	E-MEXP-1138-raw-cel-1432773130
19.9	99.6	E-MEXP-1138-raw-cel-1432773290
19.1	99.6	GSM142740	DH001_ATH1_A7-MPG1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
18.0	99.5	E-MEXP-1138-raw-cel-1432773002
17.9	99.5	GSM131638	ATGE_73_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
17.8	99.5	E-MEXP-1138-raw-cel-1432773386
17.6	99.5	E-MEXP-1138-raw-cel-1432773354
17.5	99.5	GSM131637	ATGE_73_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
16.7	99.5	E-MEXP-1138-raw-cel-1432773162
16.6	99.5	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.4	99.5	GSM142852	MG001_ATH1_A5-Torres-2N3	GSE6176	Impact of Type III effectors on plant defense responses
16.3	99.5	E-MEXP-1138-raw-cel-1432772970
16.2	99.5	GSM239251	Columbia glabrous (C24) wild type pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
16.1	99.5	E-MEXP-1138-raw-cel-1432773226
16.0	99.5	E-MEXP-285-raw-cel-440782725
15.9	99.5	GSM142853	MG001_ATH1_A6-Torres-2N6	GSE6176	Impact of Type III effectors on plant defense responses
15.2	99.4	GSM239253	CaMV::DME pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
15.1	99.4	GSM154506	Arabidopsis hydrated pollen grains rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
14.9	99.4	GSM131636	ATGE_73_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
14.8	99.4	E-MEXP-285-raw-cel-440782791
14.6	99.4	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.1	99.4	GSM131113	AtGen_B-41_3-6-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
12.8	99.3	GSM142739	DH001_ATH1_A6-TCP2	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
12.6	99.3	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.6	99.3	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.1	99.3	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.0	99.3	E-MEXP-807-raw-cel-1173273144
11.9	99.3	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.7	99.3	GSM131139	AtGen_B-25_2-4-4_REP2_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
11.6	99.3	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.0	99.2	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.9	99.2	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.7	99.2	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.5	99.2	GSM239252	Columbia glabrous (C24) wild type stamen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
10.4	99.2	GSM131111	AtGen_B-39_3-4-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
10.0	99.2	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0	99.2	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0	99.2	GSM131141	AtGen_B-27_2-6-4_REP2_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
9.7	99.1	E-MEXP-807-raw-cel-1173273196
9.5	99.1	GSM131537	ATGE_25_A	GSE5630	AtGenExpress: Developmental series (leaves)
9.5	99.1	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.2	99.1	GSM131112	AtGen_B-40_3-5-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
9.1	99.1	GSM269821	WT leaf-drought-rep2	GSE10670	Global expression profiling of wild type and transgenic Arabidopsis plants in response to water stress
9.1	99.1	GSM131606	ATGE_42_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
9.0	99.1	GSM131148	AtGen_B-34_3-6-1_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
9.0	99.1	GSM239254	CaMV::DME stamen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
8.9	99.0	GSM131607	ATGE_42_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
8.8	99.0	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
8.7	99.0	GSM133731	Buchanan-Wollaston_A-3-bwoll-C0S_SLD	GSE5727	The effects of mutants in stress response pathways on gene expression during senescence
8.7	99.0	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.6	99.0	GSM106916	opr3_JA_22 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.042	1	GO:0015986	The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.
0.016	1	GO:0016192	The directed movement of substances into, out of or within a cell by a cellular process that begins with the formation of membrane-bounded vesicles in which the transported substances are enclosed or located in the vesicle membrane. Vesicles are then targeted to, and fuse with, an acceptor membrane.
0.012	1	GO:0006886	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.

KEGG PATHWAY inferred to related to the module

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.014	1	00190	Oxidative phosphorylation
0.002	1	01100	Metabolic pathways

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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