CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g65950

Gene name unknown protein

Module size 7 genes

NF 0.63

%ile 84.0

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
0.57 73.8 1.00 At5g65950 836725 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOP O.I. H.G. S.X.
0.75 86.9 0.95 At4g24840 828587 - F:molecular_function unknown;P:protein transport, Golgi organization;C:vacuole;MFOP O.I. H.G. S.X.
0.71 84.2 0.95 At5g63840 836504 RSW3 (RADIAL SWELLING 3) radial swelling mutant shown to be specifically impaired in cellulose production. Encodes the alpha-subunit of a glucosidase II enzyme. O.I. H.G. S.X.
0.67 81.6 0.95 At4g34450 829596 coatomer gamma-2 subunit, putative / gamma-2 coat protein, putative / gamma-2 COP, putative F:protein binding, clathrin binding, structural molecule activity, binding;P:intracellular protein transport, vesicle-mediated transport;C:chloroplast, membrane;MFOPB O.I. H.G. S.X.
0.67 81.6 0.95 At5g61970 836318 signal recognition particle-related / SRP-related F:unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBA O.I. H.G. S.X.
0.50 65.3 0.95 At2g21390 816678 coatomer protein complex, subunit alpha, putative F:protein binding, structural molecule activity, transporter activity;P:intracellular protein transport, vesicle-mediated transport, ER to Golgi vesicle-mediated transport;C:COPI vesicle coat, CUL4 RING ubiquitin ligase complex, membrane;MFOBPA O.I. H.G. S.X.
0.50 65.3 0.94 At3g26370 822241 unknown protein F:unknown;P:unknown;C:Golgi apparatus;P O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.57	73.8	1.00	At5g65950	836725	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOP	O.I.	H.G.	S.X.
0.75	86.9	0.95	At4g24840	828587	-	F:molecular_function unknown;P:protein transport, Golgi organization;C:vacuole;MFOP	O.I.	H.G.	S.X.
0.71	84.2	0.95	At5g63840	836504	RSW3 (RADIAL SWELLING 3)	radial swelling mutant shown to be specifically impaired in cellulose production. Encodes the alpha-subunit of a glucosidase II enzyme.	O.I.	H.G.	S.X.
0.67	81.6	0.95	At4g34450	829596	coatomer gamma-2 subunit, putative / gamma-2 coat protein, putative / gamma-2 COP, putative	F:protein binding, clathrin binding, structural molecule activity, binding;P:intracellular protein transport, vesicle-mediated transport;C:chloroplast, membrane;MFOPB	O.I.	H.G.	S.X.
0.67	81.6	0.95	At5g61970	836318	signal recognition particle-related / SRP-related	F:unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBA	O.I.	H.G.	S.X.
0.50	65.3	0.95	At2g21390	816678	coatomer protein complex, subunit alpha, putative	F:protein binding, structural molecule activity, transporter activity;P:intracellular protein transport, vesicle-mediated transport, ER to Golgi vesicle-mediated transport;C:COPI vesicle coat, CUL4 RING ubiquitin ligase complex, membrane;MFOBPA	O.I.	H.G.	S.X.
0.50	65.3	0.94	At3g26370	822241	unknown protein	F:unknown;P:unknown;C:Golgi apparatus;P	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
70.0 99.9 GSM270814 Arabidopsis cell culture, 4 h_control_rep1 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
60.3 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
58.1 99.8 E-MEXP-1474-raw-cel-1593932929
56.9 99.8 E-MEXP-1474-raw-cel-1593932865
48.3 99.8 E-MEXP-1474-raw-cel-1593932801
26.0 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
25.9 99.7 E-MEXP-739-raw-cel-1099467419
23.8 99.6 E-MEXP-807-raw-cel-1173273060
22.7 99.6 E-MEXP-1474-raw-cel-1593932897
22.3 99.6 E-MEXP-807-raw-cel-1173273116
20.8 99.6 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
20.7 99.6 E-MEXP-739-raw-cel-1099467470
20.7 99.6 E-MEXP-1474-raw-cel-1593932769
19.8 99.6 GSM47022 Col-0 12 GSE2473 Small RNA biogenesis mutants
19.5 99.6 E-MEXP-807-raw-cel-1173273223
18.9 99.5 E-MEXP-739-raw-cel-1099467436
18.4 99.5 E-MEXP-739-raw-cel-1099467402
17.2 99.5 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.0 99.5 E-MEXP-739-raw-cel-1099467453
16.9 99.5 E-MEXP-739-raw-cel-1099467487
15.7 99.5 GSM47020 Col-0 10 GSE2473 Small RNA biogenesis mutants
15.0 99.4 E-MEXP-807-raw-cel-1173273144
14.9 99.4 E-MEXP-807-raw-cel-1173273170
14.9 99.4 GSM270866 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep1 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
14.4 99.4 GSM47021 Col-0 11 GSE2473 Small RNA biogenesis mutants
14.2 99.4 GSM322555 genotype: ataf1-1 mutant, ecotype Col-0 - treated or untreated: Bgh inoculated - rep2 GSE12856 Penetration resistance: Wildtype and ataf1-1 mutant response to Bgh 12 h after inoculation, 22 factorial design
13.4 99.4 GSM47047 rdr2-1 37 GSE2473 Small RNA biogenesis mutants
13.2 99.4 GSM128727 Pieterse_1-13_Mpersicae-48h_Rep1_ATH1 GSE5525 Transcriptome changes of Arabidopsis during pathogen and insect attack
13.0 99.4 GSM134202 Murray_3-1_D1-GROWTH_Rep1_ATH1 GSE5750 Growth of suspension-cultured cells
13.0 99.4 E-MEXP-807-raw-cel-1173273252
12.6 99.3 GSM142853 MG001_ATH1_A6-Torres-2N6 GSE6176 Impact of Type III effectors on plant defense responses
12.4 99.3 GSM142852 MG001_ATH1_A5-Torres-2N3 GSE6176 Impact of Type III effectors on plant defense responses
12.3 99.3 E-MEXP-807-raw-cel-1173273088
12.2 99.3 GSM184482 Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
11.8 99.3 GSM134208 Murray_3-4_D7-GROWTH_Rep1_ATH1 GSE5750 Growth of suspension-cultured cells
11.3 99.3 GSM128728 Pieterse_1-14_Mpersicae-72h_Rep1_ATH1 GSE5525 Transcriptome changes of Arabidopsis during pathogen and insect attack
10.7 99.2 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.1 99.2 GSM322556 genotype: ataf1-1 mutant, ecotype Col-0 - treated or untreated: Bgh inoculated - rep3 GSE12856 Penetration resistance: Wildtype and ataf1-1 mutant response to Bgh 12 h after inoculation, 22 factorial design
10.1 99.2 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.0 99.2 GSM270853 Arabidopsis cell culture, 4 h_control_rep2 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
9.9 99.1 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9 99.1 GSM142850 MG001_ATH1_A3-Torres-1N6 GSE6176 Impact of Type III effectors on plant defense responses
9.2 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
8.9 99.0 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
8.8 99.0 GSM142849 MG001_ATH1_A2-Torres-1N3 GSE6176 Impact of Type III effectors on plant defense responses

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
70.0	99.9	GSM270814	Arabidopsis cell culture, 4 h_control_rep1	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
60.3	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
58.1	99.8	E-MEXP-1474-raw-cel-1593932929
56.9	99.8	E-MEXP-1474-raw-cel-1593932865
48.3	99.8	E-MEXP-1474-raw-cel-1593932801
26.0	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
25.9	99.7	E-MEXP-739-raw-cel-1099467419
23.8	99.6	E-MEXP-807-raw-cel-1173273060
22.7	99.6	E-MEXP-1474-raw-cel-1593932897
22.3	99.6	E-MEXP-807-raw-cel-1173273116
20.8	99.6	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
20.7	99.6	E-MEXP-739-raw-cel-1099467470
20.7	99.6	E-MEXP-1474-raw-cel-1593932769
19.8	99.6	GSM47022	Col-0 12	GSE2473	Small RNA biogenesis mutants
19.5	99.6	E-MEXP-807-raw-cel-1173273223
18.9	99.5	E-MEXP-739-raw-cel-1099467436
18.4	99.5	E-MEXP-739-raw-cel-1099467402
17.2	99.5	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.0	99.5	E-MEXP-739-raw-cel-1099467453
16.9	99.5	E-MEXP-739-raw-cel-1099467487
15.7	99.5	GSM47020	Col-0 10	GSE2473	Small RNA biogenesis mutants
15.0	99.4	E-MEXP-807-raw-cel-1173273144
14.9	99.4	E-MEXP-807-raw-cel-1173273170
14.9	99.4	GSM270866	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep1	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
14.4	99.4	GSM47021	Col-0 11	GSE2473	Small RNA biogenesis mutants
14.2	99.4	GSM322555	genotype: ataf1-1 mutant, ecotype Col-0 - treated or untreated: Bgh inoculated - rep2	GSE12856	Penetration resistance: Wildtype and ataf1-1 mutant response to Bgh 12 h after inoculation, 2*2 factorial design
13.4	99.4	GSM47047	rdr2-1 37	GSE2473	Small RNA biogenesis mutants
13.2	99.4	GSM128727	Pieterse_1-13_Mpersicae-48h_Rep1_ATH1	GSE5525	Transcriptome changes of Arabidopsis during pathogen and insect attack
13.0	99.4	GSM134202	Murray_3-1_D1-GROWTH_Rep1_ATH1	GSE5750	Growth of suspension-cultured cells
13.0	99.4	E-MEXP-807-raw-cel-1173273252
12.6	99.3	GSM142853	MG001_ATH1_A6-Torres-2N6	GSE6176	Impact of Type III effectors on plant defense responses
12.4	99.3	GSM142852	MG001_ATH1_A5-Torres-2N3	GSE6176	Impact of Type III effectors on plant defense responses
12.3	99.3	E-MEXP-807-raw-cel-1173273088
12.2	99.3	GSM184482	Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.8	99.3	GSM134208	Murray_3-4_D7-GROWTH_Rep1_ATH1	GSE5750	Growth of suspension-cultured cells
11.3	99.3	GSM128728	Pieterse_1-14_Mpersicae-72h_Rep1_ATH1	GSE5525	Transcriptome changes of Arabidopsis during pathogen and insect attack
10.7	99.2	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.1	99.2	GSM322556	genotype: ataf1-1 mutant, ecotype Col-0 - treated or untreated: Bgh inoculated - rep3	GSE12856	Penetration resistance: Wildtype and ataf1-1 mutant response to Bgh 12 h after inoculation, 2*2 factorial design
10.1	99.2	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.0	99.2	GSM270853	Arabidopsis cell culture, 4 h_control_rep2	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
9.9	99.1	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9	99.1	GSM142850	MG001_ATH1_A3-Torres-1N6	GSE6176	Impact of Type III effectors on plant defense responses
9.2	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
8.9	99.0	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
8.8	99.0	GSM142849	MG001_ATH1_A2-Torres-1N3	GSE6176	Impact of Type III effectors on plant defense responses

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.154 1 GO:0007030 A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
0.065 1 GO:0006888 The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
0.057 1 GO:0030244 The chemical reactions and pathways resulting in the formation of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.

SF	Genes	GO ID	Process Name
0.154	1	GO:0007030	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.
0.065	1	GO:0006888	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
0.057	1	GO:0030244	The chemical reactions and pathways resulting in the formation of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.061 1 03060 Protein export
0.050 1 00052 Galactose metabolism
0.022 1 00500 Starch and sucrose metabolism

SF	Genes	KEGG ID	Pathway name
0.061	1	03060	Protein export
0.050	1	00052	Galactose metabolism
0.022	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	At5g65950
Gene name	unknown protein
Module size	7 genes
NF	0.63
%ile	84.0

Co-expression analysis

Gene ID At5g65950 Gene name unknown protein Module size 7 genes NF 0.63 %ile 84.0

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 KEGG0.061103060Protein export0.050100052Galactose metabolism0.022100500Starch 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 At5g65950

Gene name unknown protein

Module size 7 genes

NF 0.63

%ile 84.0

: 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
0.061 1 03060 Protein export
0.050 1 00052 Galactose metabolism
0.022 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