CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g04950

Gene name NAS1 (NICOTIANAMINE SYNTHASE 1)

Module size 6 genes

NF 0.07

%ile 4.0

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
0.20 14.4 1.00 At5g04950 830377 NAS1 (NICOTIANAMINE SYNTHASE 1) Encodes a nicotianamide synthase. O.I. H.G. S.X.
0.33 38.1 0.67 At1g74760 - - O.I. H.G. S.X.
0.33 38.1 0.66 At3g58810 825050 MTPA2 (METAL TOLERANCE PROTEIN A2) Member of Zinc transporter (ZAT) family. Contributes to basic cellular Zn tolerance and controls Zn partitioning, particularly under conditions of high rates of Zn influx into the root symplasm. Localizes to the vacuolar membrane. O.I. H.G. S.X.
0.29 30.3 0.68 At3g46900 823843 COPT2 encodes a member of copper transporter family and functionally complements a high affinity copper transporter mutant in yeast O.I. H.G. S.X.
0.18 11.4 0.67 At5g23020 832366 IMS2 (2-ISOPROPYLMALATE SYNTHASE 2) methylthioalkymalate synthase-like. Also known as 2-isopropylmalate synthase (IMS2). encodes a methylthioalkylmalate synthase involved in the biosynthesis of aliphatic glucosinolates which accepts all the omega-methylthio-2-oxoalkanoic acids needed to form the known C3 to C8 glucosinolates in Arabidopsis. O.I. H.G. S.X.
0.02 0.4 0.65 At3g62040 825377 catalytic/ hydrolase F:hydrolase activity, catalytic activity;P:metabolic process;C:unknown;OBPFA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.20	14.4	1.00	At5g04950	830377	NAS1 (NICOTIANAMINE SYNTHASE 1)	Encodes a nicotianamide synthase.	O.I.	H.G.	S.X.
0.33	38.1	0.67	At1g74760		-	-	O.I.	H.G.	S.X.
0.33	38.1	0.66	At3g58810	825050	MTPA2 (METAL TOLERANCE PROTEIN A2)	Member of Zinc transporter (ZAT) family. Contributes to basic cellular Zn tolerance and controls Zn partitioning, particularly under conditions of high rates of Zn influx into the root symplasm. Localizes to the vacuolar membrane.	O.I.	H.G.	S.X.
0.29	30.3	0.68	At3g46900	823843	COPT2	encodes a member of copper transporter family and functionally complements a high affinity copper transporter mutant in yeast	O.I.	H.G.	S.X.
0.18	11.4	0.67	At5g23020	832366	IMS2 (2-ISOPROPYLMALATE SYNTHASE 2)	methylthioalkymalate synthase-like. Also known as 2-isopropylmalate synthase (IMS2). encodes a methylthioalkylmalate synthase involved in the biosynthesis of aliphatic glucosinolates which accepts all the omega-methylthio-2-oxoalkanoic acids needed to form the known C3 to C8 glucosinolates in Arabidopsis.	O.I.	H.G.	S.X.
0.02	0.4	0.65	At3g62040	825377	catalytic/ hydrolase	F:hydrolase activity, catalytic activity;P:metabolic process;C:unknown;OBPFA	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
79.5 99.9 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
46.3 99.8 GSM133774 Lindsey_1-26_torpedo-meristem_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
37.9 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
28.8 99.7 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
17.2 99.5 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.0 99.5 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.6 99.5 GSM176879 AWP_Control_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
15.7 99.5 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.1 99.4 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.8 99.4 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.4 99.4 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.2 99.4 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.0 99.4 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
12.8 99.3 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
12.1 99.3 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.3 99.3 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.6 99.2 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.6 99.2 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9 99.1 GSM133776 Lindsey_1-1_globular-apical_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7 99.1 GSM133770 Lindsey_1-22_torpedo-apical_Rep4_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7 99.1 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.2 99.1 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.1 99.1 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
8.6 99.0 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
8.6 99.0 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
79.5	99.9	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
46.3	99.8	GSM133774	Lindsey_1-26_torpedo-meristem_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
37.9	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
28.8	99.7	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
17.2	99.5	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.0	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.6	99.5	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
15.7	99.5	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.1	99.4	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.8	99.4	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.4	99.4	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.2	99.4	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.0	99.4	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
12.8	99.3	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
12.1	99.3	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.3	99.3	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.6	99.2	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.6	99.2	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9	99.1	GSM133776	Lindsey_1-1_globular-apical_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7	99.1	GSM133770	Lindsey_1-22_torpedo-apical_Rep4_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.7	99.1	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.2	99.1	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.1	99.1	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
8.6	99.0	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
8.6	99.0	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.286 1 GO:0010299 Any process that reduces or removes the toxicity of cobalt ion. These include transport of cobalt away from sensitive areas and to compartments or complexes whose purpose is sequestration of cobalt ion.
0.286 1 GO:0010312 Any process that reduces or removes the toxicity of zinc ion. These include transport of zinc away from sensitive areas and to compartments or complexes whose purpose is sequestration of zinc ion.
0.286 1 GO:0015678 The directed, high-affinity movement of copper (Cu) ions into, out of, within or between cells. In high affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations.

SF	Genes	GO ID	Process Name
0.286	1	GO:0010299	Any process that reduces or removes the toxicity of cobalt ion. These include transport of cobalt away from sensitive areas and to compartments or complexes whose purpose is sequestration of cobalt ion.
0.286	1	GO:0010312	Any process that reduces or removes the toxicity of zinc ion. These include transport of zinc away from sensitive areas and to compartments or complexes whose purpose is sequestration of zinc ion.
0.286	1	GO:0015678	The directed, high-affinity movement of copper (Cu) ions into, out of, within or between cells. In high affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.074 1 00966 Glucosinolate biosynthesis
0.054 1 00290 Valine, leucine and isoleucine biosynthesis
0.028 1 00620 Pyruvate metabolism

SF	Genes	KEGG ID	Pathway name
0.074	1	00966	Glucosinolate biosynthesis
0.054	1	00290	Valine, leucine and isoleucine biosynthesis
0.028	1	00620	Pyruvate 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

Back to the CoP portal site

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Gene ID	At5g04950
Gene name	NAS1 (NICOTIANAMINE SYNTHASE 1)
Module size	6 genes
NF	0.07
%ile	4.0

Co-expression analysis

Gene ID At5g04950 Gene name NAS1 (NICOTIANAMINE SYNTHASE 1) Module size 6 genes NF 0.07 %ile 4.0

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 More genes

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Biological processes inferred to relate to the module

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.074100966Glucosinolate biosynthesis0.054100290Valine, leucine and isoleucine biosynthesis0.028100620Pyruvate metabolism

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Glycine_maxHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID At5g04950

Gene name NAS1 (NICOTIANAMINE SYNTHASE 1)

Module size 6 genes

NF 0.07

%ile 4.0

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes KEGG ID Pathway name Link to KEGG
0.074 1 00966 Glucosinolate biosynthesis
0.054 1 00290 Valine, leucine and isoleucine biosynthesis
0.028 1 00620 Pyruvate metabolism

Select a plant to compare co-expressed genes between species.
Glycine_max
Hordeum_vulgare
Oryza_sativa
Populus_trichocarpa
Triticum_aestivum
Vitis_vinifera
Zea_mays