CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g62040

Gene name catalytic/ hydrolase

Module size 5 genes

NF 0.58

%ile 79.3

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
0.67 81.6 1.00 At3g62040 825377 catalytic/ hydrolase F:hydrolase activity, catalytic activity;P:metabolic process;C:unknown;OBPFA O.I. H.G. S.X.
0.75 86.9 0.82 At2g28780 817427 unknown protein F:unknown;P:biological_process unknown;C:mitochondrion;BPO O.I. H.G. S.X.
0.67 81.6 0.88 At1g32450 840139 NRT1.5 (NITRATE TRANSPORTER 1.5) Transmembrane nitrate transporter. Involved in xylem transport of nitrate from root to shoot. Induced in response to nitrate. Not involved in nitrate uptake. expressed in root pericycle cells. O.I. H.G. S.X.
0.50 65.3 0.81 At5g43180 834336 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PBO O.I. H.G. S.X.
0.43 55.3 0.82 At4g33420 829479 peroxidase, putative F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:unknown;PFOBM O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.67	81.6	1.00	At3g62040	825377	catalytic/ hydrolase	F:hydrolase activity, catalytic activity;P:metabolic process;C:unknown;OBPFA	O.I.	H.G.	S.X.
0.75	86.9	0.82	At2g28780	817427	unknown protein	F:unknown;P:biological_process unknown;C:mitochondrion;BPO	O.I.	H.G.	S.X.
0.67	81.6	0.88	At1g32450	840139	NRT1.5 (NITRATE TRANSPORTER 1.5)	Transmembrane nitrate transporter. Involved in xylem transport of nitrate from root to shoot. Induced in response to nitrate. Not involved in nitrate uptake. expressed in root pericycle cells.	O.I.	H.G.	S.X.
0.50	65.3	0.81	At5g43180	834336	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PBO	O.I.	H.G.	S.X.
0.43	55.3	0.82	At4g33420	829479	peroxidase, putative	F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:unknown;PFOBM	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
70.2 99.9 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.7 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.1 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.3 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.1 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
62.8 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.7 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.5 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.7 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
60.7 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.5 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
55.2 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.8 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
53.3 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
53.2 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
51.2 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
50.6 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
47.1 99.8 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
42.7 99.8 GSM133962 Fukuda_1-7_6A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
41.8 99.8 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
41.1 99.8 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
40.3 99.8 GSM133963 Fukuda_1-8_6B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
34.7 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.7 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
28.4 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.7 99.7 GSM142750 MJ001_ATH1_A1-jones-WT1 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
22.7 99.6 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.4 99.6 GSM142751 MJ001_ATH1_A2-jones-WT2 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
20.8 99.6 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.4 99.6 GSM133961 Fukuda_1-6_4B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
16.6 99.5 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
15.4 99.5 GSM284386 Arabidopsis GSUS3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
14.8 99.4 GSM133960 Fukuda_1-5_4A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
14.3 99.4 GSM133965 Fukuda_1-10_8B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
12.1 99.3 GSM142754 MJ001_ATH1_A5-jones-WT-Rep3 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
12.1 99.3 GSM133964 Fukuda_1-9_8A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.8 99.1 GSM131106 Broadley_1-4_A4-Bo-P3-phosphate-starved_Rep3_ATH1 GSE5614 Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)
9.4 99.1 E-MEXP-1592-raw-cel-1617526984
9.3 99.1 GSM184552 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.2 99.1 GSM176879 AWP_Control_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.8 99.0 GSM176880 AWP_Control_2 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.6 99.0 E-MEXP-509-raw-cel-829148525

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
70.2	99.9	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.7	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.1	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.3	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.1	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
62.8	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.7	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.5	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.7	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
60.7	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.5	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
55.2	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
54.8	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
53.3	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
53.2	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
51.2	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.6	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
47.1	99.8	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
42.7	99.8	GSM133962	Fukuda_1-7_6A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
41.8	99.8	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
41.1	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
40.3	99.8	GSM133963	Fukuda_1-8_6B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
34.7	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.7	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
28.4	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.7	99.7	GSM142750	MJ001_ATH1_A1-jones-WT1	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
22.7	99.6	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.4	99.6	GSM142751	MJ001_ATH1_A2-jones-WT2	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
20.8	99.6	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.4	99.6	GSM133961	Fukuda_1-6_4B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
16.6	99.5	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
15.4	99.5	GSM284386	Arabidopsis GSUS3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
14.8	99.4	GSM133960	Fukuda_1-5_4A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
14.3	99.4	GSM133965	Fukuda_1-10_8B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
12.1	99.3	GSM142754	MJ001_ATH1_A5-jones-WT-Rep3	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
12.1	99.3	GSM133964	Fukuda_1-9_8A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.8	99.1	GSM131106	Broadley_1-4_A4-Bo-P3-phosphate-starved_Rep3_ATH1	GSE5614	Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)
9.4	99.1	E-MEXP-1592-raw-cel-1617526984
9.3	99.1	GSM184552	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.2	99.1	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.8	99.0	GSM176880	AWP_Control_2	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
8.6	99.0	E-MEXP-509-raw-cel-829148525

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.143 1 GO:0015706 The directed movement of nitrate into, out of, within or between cells.
0.143 1 GO:0042128 The uptake, from the environment, of nitrates, inorganic or organic salts and esters of nitric acid and the subsequent reduction of nitrate ion to other, less highly oxidized, inorganic nitrogenous substances.
0.100 1 GO:0010167 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrate stimulus.

SF	Genes	GO ID	Process Name
0.143	1	GO:0015706	The directed movement of nitrate into, out of, within or between cells.
0.143	1	GO:0042128	The uptake, from the environment, of nitrates, inorganic or organic salts and esters of nitric acid and the subsequent reduction of nitrate ion to other, less highly oxidized, inorganic nitrogenous substances.
0.100	1	GO:0010167	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrate stimulus.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.024 1 00360 Phenylalanine metabolism
0.023 1 00680 Methane metabolism
0.019 1 00940 Phenylpropanoid biosynthesis

SF	Genes	KEGG ID	Pathway name
0.024	1	00360	Phenylalanine metabolism
0.023	1	00680	Methane metabolism
0.019	1	00940	Phenylpropanoid biosynthesis

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	At3g62040
Gene name	catalytic/ hydrolase
Module size	5 genes
NF	0.58
%ile	79.3

Co-expression analysis

Gene ID At3g62040 Gene name catalytic/ hydrolase Module size 5 genes NF 0.58 %ile 79.3

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 KEGG0.024100360Phenylalanine metabolism0.023100680Methane metabolism0.019100940Phenylpropanoid biosynthesis

Inter-species module comparison

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

Gene ID At3g62040

Gene name catalytic/ hydrolase

Module size 5 genes

NF 0.58

%ile 79.3

: 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
0.024 1 00360 Phenylalanine metabolism
0.023 1 00680 Methane metabolism
0.019 1 00940 Phenylpropanoid biosynthesis

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