CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g26560

Gene name BGLU40 (BETA GLUCOSIDASE 40)

Module size 6 genes

NF 0.10

%ile 6.8

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 At1g26560 839196 BGLU40 (BETA GLUCOSIDASE 40) F:cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:apoplast, chloroplast;BOPMFA O.I. H.G. S.X.
0.22 17.5 0.82 At5g57030 835806 LUT2 (LUTEIN DEFICIENT 2) Lutein-deficient 2 (LUT2) required for lutein biosynthesis, member of the xanthophyll class of carotenoids. Encodes lycopene epsilon cyclase O.I. H.G. S.X.
0.07 1.9 0.82 At3g01180 820294 AtSS2 (starch synthase 2) F:transferase activity, transferring glycosyl groups;P:cellulose biosynthetic process, glucan biosynthetic process, biosynthetic process, glycogen biosynthetic process;C:chloroplast;OPBMFAV O.I. H.G. S.X.
0.07 1.9 0.84 At4g34240 829573 ALDH3I1 (ALDEHYDE DEHYDROGENASE 3|1) Aldehyde dehydrogenase induced by ABA and dehydration O.I. H.G. S.X.
0.06 1.4 0.82 At5g17230 831587 phytoene synthase (PSY) / geranylgeranyl-diphosphate geranylgeranyl transferase Encodes phytoene synthase. O.I. H.G. S.X.
0.05 1.1 0.82 At5g09870 830847 CESA5 (CELLULOSE SYNTHASE 5) Encodes a cellulose synthase isomer, related to CESA6. 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	At1g26560	839196	BGLU40 (BETA GLUCOSIDASE 40)	F:cation binding, hydrolase activity, hydrolyzing O-glycosyl compounds, catalytic activity;P:carbohydrate metabolic process;C:apoplast, chloroplast;BOPMFA	O.I.	H.G.	S.X.
0.22	17.5	0.82	At5g57030	835806	LUT2 (LUTEIN DEFICIENT 2)	Lutein-deficient 2 (LUT2) required for lutein biosynthesis, member of the xanthophyll class of carotenoids. Encodes lycopene epsilon cyclase	O.I.	H.G.	S.X.
0.07	1.9	0.82	At3g01180	820294	AtSS2 (starch synthase 2)	F:transferase activity, transferring glycosyl groups;P:cellulose biosynthetic process, glucan biosynthetic process, biosynthetic process, glycogen biosynthetic process;C:chloroplast;OPBMFAV	O.I.	H.G.	S.X.
0.07	1.9	0.84	At4g34240	829573	ALDH3I1 (ALDEHYDE DEHYDROGENASE 3\|1)	Aldehyde dehydrogenase induced by ABA and dehydration	O.I.	H.G.	S.X.
0.06	1.4	0.82	At5g17230	831587	phytoene synthase (PSY) / geranylgeranyl-diphosphate geranylgeranyl transferase	Encodes phytoene synthase.	O.I.	H.G.	S.X.
0.05	1.1	0.82	At5g09870	830847	CESA5 (CELLULOSE SYNTHASE 5)	Encodes a cellulose synthase isomer, related to CESA6.	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
83.8 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
58.4 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
52.2 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.8 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
49.2 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
49.2 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.6 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.5 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.2 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.8 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
43.7 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.5 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.7 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.5 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.9 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
40.8 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.2 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.1 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.7 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.9 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
33.3 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.6 99.7 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
20.7 99.6 GSM270870 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
16.1 99.5 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
13.4 99.4 GSM270868 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
12.8 99.3 GSM133957 Fukuda_1-2_0B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.8 99.3 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
11.4 99.3 GSM128661 Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
11.1 99.2 GSM128676 Underwood_1-29_DC3000-10e8-7h_Rep2_ATH1 GSE5520 Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.1 99.2 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
83.8	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
58.4	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.2	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.8	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
49.2	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
49.2	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.6	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.5	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.2	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.8	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
43.7	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.5	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.7	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.5	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.9	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
40.8	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.2	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.1	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.7	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.9	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
33.3	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.6	99.7	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
20.7	99.6	GSM270870	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
16.1	99.5	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
13.4	99.4	GSM270868	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
12.8	99.3	GSM133957	Fukuda_1-2_0B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.8	99.3	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
11.4	99.3	GSM128661	Underwood_1-14_Cor-5x10e7-10h_Rep2_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
11.1	99.2	GSM128676	Underwood_1-29_DC3000-10e8-7h_Rep2_ATH1	GSE5520	Genome-wide transcriptional analysis of the compatible A. thaliana-P. syringae pv. tomato DC3000 interaction
10.1	99.2	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.250 1 GO:0009250 The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
0.211 2 GO:0016117 The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.
0.167 1 GO:0016120 The chemical reactions and pathways resulting in the formation of carotenes, hydrocarbon carotenoids.

SF	Genes	GO ID	Process Name
0.250	1	GO:0009250	The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
0.211	2	GO:0016117	The chemical reactions and pathways resulting in the formation of carotenoids, tetraterpenoid compounds in which two units of 4 isoprenoid residues joined head-to-tail are themselves joined tail-to-tail.
0.167	1	GO:0016120	The chemical reactions and pathways resulting in the formation of carotenes, hydrocarbon carotenoids.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.143 2 00906 Carotenoid biosynthesis
0.100 1 00340 Histidine metabolism
0.095 1 00310 Lysine degradation

SF	Genes	KEGG ID	Pathway name
0.143	2	00906	Carotenoid biosynthesis
0.100	1	00340	Histidine metabolism
0.095	1	00310	Lysine degradation

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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Gene ID	At1g26560
Gene name	BGLU40 (BETA GLUCOSIDASE 40)
Module size	6 genes
NF	0.10
%ile	6.8

Co-expression analysis

Gene ID At1g26560 Gene name BGLU40 (BETA GLUCOSIDASE 40) Module size 6 genes NF 0.10 %ile 6.8

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 KEGG0.143200906Carotenoid biosynthesis0.100100340Histidine metabolism0.095100310Lysine degradation

Inter-species module comparison

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

Gene ID At1g26560

Gene name BGLU40 (BETA GLUCOSIDASE 40)

Module size 6 genes

NF 0.10

%ile 6.8

: 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
0.143 2 00906 Carotenoid biosynthesis
0.100 1 00340 Histidine metabolism
0.095 1 00310 Lysine degradation

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