Co-expression analysis

Gene ID	At3g25930
Gene name	universal stress protein (USP) family protein
Module size	5 genes
NF	0.37
%ile	51.0

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
0.17	10.2	1.00	At3g25930	822190	universal stress protein (USP) family protein	F:molecular_function unknown;P:response to stress;C:cellular_component unknown;P	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)
0.61	76.7	0.81	At4g37060	829860	PLP5 (PATATIN-LIKE PROTEIN 5)	F:nutrient reservoir activity;P:metabolic process, lipid metabolic process;C:cellular_component unknown;PBOMF	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)
0.55	70.6	0.77	At3g01420	821135	DOX1	Encodes an alpha-dioxygenase involved in protection against oxidative stress and cell death. Induced in response to Salicylic acid and oxidative stress. Independent of NPR1 in induction by salicylic acid.	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)
0.55	70.6	0.80	At4g37010	829855	caltractin, putative / centrin, putative	F:calcium ion binding;P:biological_process unknown;C:unknown;MFPOB	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)
0.40	50.8	0.78	At3g09220	820078	LAC7 (laccase 7)	putative laccase, a member of laccase family of genes (17 members in Arabidopsis).	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
94.5	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
85.9	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
83.6	99.9	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
80.3	99.9	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
80.1	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
76.6	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
73.8	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
73.7	99.9	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
72.4	99.9	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
68.9	99.9	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.5	99.9	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
65.7	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.2	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
64.6	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.9	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.3	99.8	GSM184556	Whole roots 2hr KNO3 treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
61.8	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
56.7	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.6	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.7	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
44.3	99.8	GSM184908	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
43.1	99.8	GSM184900	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
42.8	99.8	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
40.0	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
33.1	99.7	GSM184907	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
31.8	99.7	GSM266662	Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
31.5	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
29.2	99.7	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
27.8	99.7	GSM106833	opr3_JA_0.5 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
27.3	99.7	GSM266663	Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
25.9	99.7	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
25.7	99.7	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.2	99.6	GSM106825	opr3_0 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
23.5	99.6	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
22.7	99.6	GSM106919	opr3_OPDA_0.5 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
21.6	99.6	GSM184909	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
21.1	99.6	GSM266664	Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
20.9	99.6	GSM133985	Birnbaum_1-15_StageIII-4_Rep4_ATH1	GSE5749	A gene expression map of the Arabidopsis root
20.5	99.6	GSM184912	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
20.0	99.6	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
19.7	99.6	GSM184921	Arabidopsis, root cells, stele, 140 mM NaCls, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
19.6	99.6	GSM106924	opr3_OPDA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
19.2	99.6	GSM133983	Birnbaum_1-13_StageIII-2_Rep2_ATH1	GSE5749	A gene expression map of the Arabidopsis root
19.0	99.5	GSM106908	opr3_JA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
18.9	99.5	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
17.6	99.5	GSM106921	opr3_OPDA_0.5 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
17.6	99.5	GSM184889	Arabidopsis, root cells, epidermis and lateral root cap, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
17.5	99.5	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.3	99.5	GSM184890	Arabidopsis, root cells, epidermis and lateral root cap, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
16.4	99.5	GSM106966	opr3_OPDA_8 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
16.0	99.5	GSM133975	Birnbaum_1-5_StageI-2_Rep2_ATH1	GSE5749	A gene expression map of the Arabidopsis root
15.8	99.5	GSM131611	ATGE_43_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
15.7	99.5	GSM184891	Arabidopsis, root cells, epidermis and lateral root cap, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
15.6	99.5	GSM131609	ATGE_43_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
15.1	99.4	GSM133970	Birnbaum_1-21_LRC-3_Rep3_ATH1	GSE5749	A gene expression map of the Arabidopsis root
14.7	99.4	GSM184894	Arabidopsis, root cells, columella root cap, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
14.7	99.4	GSM106922	opr3_OPDA_2 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.6	99.4	GSM106920	opr3_OPDA_0.5 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.1	99.4	GSM266676	Arabidopsis, root cells, stele, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
14.0	99.4	GSM106827	opr3_0 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
13.2	99.4	GSM131610	ATGE_43_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
13.2	99.4	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
12.8	99.3	GSM265430	Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.8	99.3	GSM131607	ATGE_42_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
12.7	99.3	GSM265431	Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.6	99.3	GSM131606	ATGE_42_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
12.4	99.3	GSM106934	opr3_OPDA_8 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
12.4	99.3	GSM176878	AWP_AL_Txed_2	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
12.2	99.3	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
12.1	99.3	GSM131454	AtGen_6-9322_Heatstress-Roots-3.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
12.1	99.3	GSM131608	ATGE_42_D	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
12.0	99.3	GSM106911	opr2_JA_2 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
12.0	99.3	GSM184893	Arabidopsis, root cells, columella root cap, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
11.9	99.3	GSM266665	Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 4	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
11.9	99.3	GSM184839	Arabidopsis, root, longitudinal zone 1, standard conditions, NaCl, replicate 1	GSE7639	Expression analysis of root developmental zones after treatment with salt
11.9	99.3	GSM106828	opr3_0 hr_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.8	99.3	GSM266668	Arabidopsis, root cells, columella root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
11.6	99.3	GSM184633	Arabidopsis, whole roots, 140 mM NaCl, replicate 2	GSE7636	Expression analysis of the effect of protoplasting and FACS sorting in roots
11.1	99.2	GSM266673	Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
10.0	99.2	GSM184494	Endodermis&Pericycle root cells 2hr KCl control treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.0	99.2	GSM131453	AtGen_6-9321_Heatstress-Roots-3.0h_Rep1	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
9.7	99.1	GSM265413	Arabidopsis, whole roots, -Fe, replicate 3	GSE10496	Expression analysis of the effect of protoplasting and FACS sorting in roots exposed to iron deficiency (-Fe)
9.7	99.1	GSM184831	Arabidopsis, root, longitudinal zone 1, standard conditions, replicate 1	GSE7639	Expression analysis of root developmental zones after treatment with salt
9.6	99.1	GSM106907	opr3_JA_0.5 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.5	99.1	GSM184899	Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
9.4	99.1	GSM131450	AtGen_6-9222_Heatstress-Roots-1.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
9.0	99.1	GSM266674	Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
8.8	99.0	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.7	99.0	GSM184840	Arabidopsis, root, longitudinal zone 1, standard conditions, NaCl, replicate 2	GSE7639	Expression analysis of root developmental zones after treatment with salt

Biological processes inferred to relate to the module

SF	Genes	GO ID	Process Name	Link to AmiGO
0.333	1	GO:0001561	A metabolic pathway by which 3-methyl branched fatty acids are degraded. These compounds are not degraded by the normal peroxisomal beta-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase. The 3-methyl branched fatty acid is converted in several steps to pristenic acid, which can then feed into the beta-oxidative pathway.
0.111	1	GO:0046274	The chemical reactions and pathways resulting in the breakdown of lignins, a class of polymers of phenylpropanoid units.
0.051	1	GO:0008219	The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.

KEGG PATHWAY inferred to related to the module

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.059	1	00592	alpha-Linolenic acid metabolism

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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