CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g52600

Gene name AtcwINV2 (Arabidopsis thaliana cell wall invertase 2)

Module size 12 genes

NF 0.54

%ile 75.8

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 At3g52600 824426 AtcwINV2 (Arabidopsis thaliana cell wall invertase 2) F:hydrolase activity, hydrolyzing O-glycosyl compounds;P:sucrose catabolic process, using beta-fructofuranosidase, carbohydrate metabolic process;C:endomembrane system;BPFOMA O.I. H.G. S.X.
0.87 93.5 0.98 At5g15110 831363 lyase/ pectate lyase F:lyase activity, pectate lyase activity;P:biological_process unknown;C:endomembrane system;PBFO O.I. H.G. S.X.
0.67 81.6 0.99 At1g11770 837722 FAD binding / catalytic/ electron carrier/ oxidoreductase F:electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity;P:unknown;C:endomembrane system;BFPOA O.I. H.G. S.X.
0.61 76.7 0.98 At1g03050 839416 epsin N-terminal homology (ENTH) domain-containing protein / clathrin assembly protein-related F:phospholipid binding, clathrin binding, binding, phosphatidylinositol binding;P:N-terminal protein myristoylation, clathrin coat assembly;C:clathrin coat;MOPFBVA O.I. H.G. S.X.
0.58 73.8 0.98 At2g46210 819228 delta-8 sphingolipid desaturase, putative F:oxidoreductase activity, oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water, iron ion binding, heme binding;P:fatty acid biosynthetic process, lipid metabolic process;C:unknown;FMOPBVA O.I. H.G. S.X.
0.57 73.8 0.98 At2g45800 819188 LIM domain-containing protein F:zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MOPF O.I. H.G. S.X.
0.50 65.3 0.99 At3g04700 819628 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.50 65.3 0.98 At3g20220 821566 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. H.G. S.X.
0.50 65.3 0.98 At3g43860 823499 AtGH9A4 (Arabidopsis thaliana Glycosyl Hydrolase 9A4) F:hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:endomembrane system;PBMOF O.I. H.G. S.X.
0.43 55.3 0.98 At5g58050 835917 SVL4 (SHV3-LIKE 4) F:kinase activity, glycerophosphodiester phosphodiesterase activity;P:glycerol metabolic process, lipid metabolic process;C:anchored to membrane;BPOMF O.I. H.G. S.X.
0.39 48.4 0.98 At5g16500 831511 protein kinase family protein F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MOPBFVA O.I. H.G. S.X.
0.35 41.6 0.98 At3g17060 820963 pectinesterase family protein F:pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFM O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	At3g52600	824426	AtcwINV2 (Arabidopsis thaliana cell wall invertase 2)	F:hydrolase activity, hydrolyzing O-glycosyl compounds;P:sucrose catabolic process, using beta-fructofuranosidase, carbohydrate metabolic process;C:endomembrane system;BPFOMA	O.I.	H.G.	S.X.
0.87	93.5	0.98	At5g15110	831363	lyase/ pectate lyase	F:lyase activity, pectate lyase activity;P:biological_process unknown;C:endomembrane system;PBFO	O.I.	H.G.	S.X.
0.67	81.6	0.99	At1g11770	837722	FAD binding / catalytic/ electron carrier/ oxidoreductase	F:electron carrier activity, oxidoreductase activity, FAD binding, catalytic activity;P:unknown;C:endomembrane system;BFPOA	O.I.	H.G.	S.X.
0.61	76.7	0.98	At1g03050	839416	epsin N-terminal homology (ENTH) domain-containing protein / clathrin assembly protein-related	F:phospholipid binding, clathrin binding, binding, phosphatidylinositol binding;P:N-terminal protein myristoylation, clathrin coat assembly;C:clathrin coat;MOPFBVA	O.I.	H.G.	S.X.
0.58	73.8	0.98	At2g46210	819228	delta-8 sphingolipid desaturase, putative	F:oxidoreductase activity, oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water, iron ion binding, heme binding;P:fatty acid biosynthetic process, lipid metabolic process;C:unknown;FMOPBVA	O.I.	H.G.	S.X.
0.57	73.8	0.98	At2g45800	819188	LIM domain-containing protein	F:zinc ion binding;P:biological_process unknown;C:cellular_component unknown;MOPF	O.I.	H.G.	S.X.
0.50	65.3	0.99	At3g04700	819628	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.50	65.3	0.98	At3g20220	821566	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	H.G.	S.X.
0.50	65.3	0.98	At3g43860	823499	AtGH9A4 (Arabidopsis thaliana Glycosyl Hydrolase 9A4)	F:hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:endomembrane system;PBMOF	O.I.	H.G.	S.X.
0.43	55.3	0.98	At5g58050	835917	SVL4 (SHV3-LIKE 4)	F:kinase activity, glycerophosphodiester phosphodiesterase activity;P:glycerol metabolic process, lipid metabolic process;C:anchored to membrane;BPOMF	O.I.	H.G.	S.X.
0.39	48.4	0.98	At5g16500	831511	protein kinase family protein	F:protein serine/threonine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:unknown;MOPBFVA	O.I.	H.G.	S.X.
0.35	41.6	0.98	At3g17060	820963	pectinesterase family protein	F:pectinesterase activity;P:cell wall modification;C:endomembrane system, cell wall, plant-type cell wall;PBFM	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
71.8 99.9 GSM284389 Arabidopsis GMPE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
59.1 99.8 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
53.1 99.8 GSM184905 Arabidopsis, root cells, protophloem, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
35.5 99.7 GSM284388 Arabidopsis GMPE1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
27.6 99.7 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
26.3 99.7 GSM184906 Arabidopsis, root cells, protophloem, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
22.2 99.6 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
22.2 99.6 GSM184904 Arabidopsis, root cells, protophloem, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
22.0 99.6 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.0 99.6 GSM184923 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
20.2 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
19.0 99.5 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.6 99.5 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.9 99.5 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.7 99.5 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.2 99.5 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.1 99.5 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.0 99.5 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.7 99.5 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.5 99.5 GSM133758 Lindsey_1-11_heart-stage-root_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
16.0 99.5 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.3 99.4 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.3 99.4 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.8 99.4 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.8 99.4 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.8 99.4 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.5 99.4 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.1 99.4 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
12.3 99.3 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.0 99.3 GSM176879 AWP_Control_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.9 99.2 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.9 99.2 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.4 99.2 GSM133760 Lindsey_1-12_heart-stage-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.4 99.2 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.3 99.2 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.7 99.0 E-MEXP-715-raw-cel-1121836247

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
71.8	99.9	GSM284389	Arabidopsis GMPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
59.1	99.8	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
53.1	99.8	GSM184905	Arabidopsis, root cells, protophloem, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
35.5	99.7	GSM284388	Arabidopsis GMPE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
27.6	99.7	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
26.3	99.7	GSM184906	Arabidopsis, root cells, protophloem, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
22.2	99.6	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
22.2	99.6	GSM184904	Arabidopsis, root cells, protophloem, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
22.0	99.6	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.0	99.6	GSM184923	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
20.2	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
19.0	99.5	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.6	99.5	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.9	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.7	99.5	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.2	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.1	99.5	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.0	99.5	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.7	99.5	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.5	99.5	GSM133758	Lindsey_1-11_heart-stage-root_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
16.0	99.5	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.3	99.4	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.3	99.4	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.8	99.4	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.8	99.4	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.8	99.4	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.5	99.4	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.1	99.4	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
12.3	99.3	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.0	99.3	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.9	99.2	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.9	99.2	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.4	99.2	GSM133760	Lindsey_1-12_heart-stage-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.4	99.2	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.3	99.2	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.7	99.0	E-MEXP-715-raw-cel-1121836247

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.077 1 GO:0048268 The process by which clathrin triskelia are assembled into the ordered structure known as a clathrin cage.
0.071 1 GO:0006071 The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
0.029 1 GO:0006633 The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.

SF	Genes	GO ID	Process Name
0.077	1	GO:0048268	The process by which clathrin triskelia are assembled into the ordered structure known as a clathrin cage.
0.071	1	GO:0006071	The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
0.029	1	GO:0006633	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.021 1 00500 Starch and sucrose metabolism

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.021	1	00500	Starch and sucrose 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

Back to the KAGIANA project homepage

Gene ID	At3g52600
Gene name	AtcwINV2 (Arabidopsis thaliana cell wall invertase 2)
Module size	12 genes
NF	0.54
%ile	75.8

Co-expression analysis

Gene ID At3g52600 Gene name AtcwINV2 (Arabidopsis thaliana cell wall invertase 2) Module size 12 genes NF 0.54 %ile 75.8

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 KEGG0.021100500Starch and sucrose 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 At3g52600

Gene name AtcwINV2 (Arabidopsis thaliana cell wall invertase 2)

Module size 12 genes

NF 0.54

%ile 75.8

: 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
0.021 1 00500 Starch and sucrose 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