CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g62690

Gene name TUB2

Module size 5 genes

NF 0.17

%ile 14.5

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 At5g62690 836390 TUB2 encodes tubulin beta-2/beta-3 chain O.I. H.G. S.X.
0.67 81.6 0.94 At3g19820 821519 DWF1 (DWARF 1) Involved in the conversion of the early brassinosteroid precursor 24-methylenecholesterol to campesterol. Brassinosteroids affect cellular elongation. Mutants have dwarf phenotype. DWF1 is a Ca2+-dependent calmodulin-binding protein. O.I. H.G. S.X.
0.50 65.3 0.93 At1g16920 838263 ATRABA1B (ARABIDOPSIS RAB GTPASE HOMOLOG A1B) small GTP-binding protein (Rab11)similar to YPT3/RAB11 proteins in yeast and mammals, respectively. YPT3/RAB11 is involved in intracellular protein trafficking. O.I. H.G. S.X.
0.10 3.4 0.93 At1g15810 838150 ribosomal protein S15 family protein F:structural constituent of ribosome;P:translation;C:small ribosomal subunit, ribosome, intracellular;BOPMF O.I. H.G. S.X.
0.06 1.4 0.93 At3g04610 819619 FLK (flowering locus KH domain) F:RNA binding, nucleic acid binding;P:positive regulation of flower development;C:nucleus;MOPFVB 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	At5g62690	836390	TUB2	encodes tubulin beta-2/beta-3 chain	O.I.	H.G.	S.X.
0.67	81.6	0.94	At3g19820	821519	DWF1 (DWARF 1)	Involved in the conversion of the early brassinosteroid precursor 24-methylenecholesterol to campesterol. Brassinosteroids affect cellular elongation. Mutants have dwarf phenotype. DWF1 is a Ca2+-dependent calmodulin-binding protein.	O.I.	H.G.	S.X.
0.50	65.3	0.93	At1g16920	838263	ATRABA1B (ARABIDOPSIS RAB GTPASE HOMOLOG A1B)	small GTP-binding protein (Rab11)similar to YPT3/RAB11 proteins in yeast and mammals, respectively. YPT3/RAB11 is involved in intracellular protein trafficking.	O.I.	H.G.	S.X.
0.10	3.4	0.93	At1g15810	838150	ribosomal protein S15 family protein	F:structural constituent of ribosome;P:translation;C:small ribosomal subunit, ribosome, intracellular;BOPMF	O.I.	H.G.	S.X.
0.06	1.4	0.93	At3g04610	819619	FLK (flowering locus KH domain)	F:RNA binding, nucleic acid binding;P:positive regulation of flower development;C:nucleus;MOPFVB	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
81.5 99.9 GSM184484 Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
78.9 99.9 GSM133759 Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
70.2 99.9 GSM184477 Lateral Root Cap root cells 2hr KCl control treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
44.5 99.8 GSM184483 Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
43.9 99.8 GSM184478 Lateral Root Cap root cells 2hr KCl control treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
28.8 99.7 GSM184481 Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
27.8 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.8 99.7 GSM184480 Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
25.2 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
25.1 99.6 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.5 99.6 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.4 99.6 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.4 99.6 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.3 99.6 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
23.2 99.6 GSM184479 Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
22.5 99.6 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.2 99.6 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.8 99.6 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.3 99.6 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.2 99.6 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.4 99.6 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.8 99.6 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.0 99.5 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.9 99.5 GSM142750 MJ001_ATH1_A1-jones-WT1 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
18.5 99.5 GSM142751 MJ001_ATH1_A2-jones-WT2 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
18.4 99.5 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.2 99.5 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.2 99.5 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.3 99.4 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
12.1 99.3 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.9 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.
10.3 99.2 GSM142730 CH001_ATH1_A009-Hampt-wsc_repeat GSE6161 Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
9.3 99.1 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
81.5	99.9	GSM184484	Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
78.9	99.9	GSM133759	Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
70.2	99.9	GSM184477	Lateral Root Cap root cells 2hr KCl control treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
44.5	99.8	GSM184483	Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
43.9	99.8	GSM184478	Lateral Root Cap root cells 2hr KCl control treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
28.8	99.7	GSM184481	Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
27.8	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.8	99.7	GSM184480	Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
25.2	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.1	99.6	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.5	99.6	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.4	99.6	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.4	99.6	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.3	99.6	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.2	99.6	GSM184479	Lateral Root Cap root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
22.5	99.6	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.2	99.6	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.8	99.6	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.3	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.2	99.6	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.4	99.6	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.8	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.0	99.5	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.9	99.5	GSM142750	MJ001_ATH1_A1-jones-WT1	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
18.5	99.5	GSM142751	MJ001_ATH1_A2-jones-WT2	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
18.4	99.5	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.2	99.5	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.2	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.3	99.4	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
12.1	99.3	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.9	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.
10.3	99.2	GSM142730	CH001_ATH1_A009-Hampt-wsc_repeat	GSE6161	Differential gene expression patterns in Arabidopsis mutants lacking the K+ channels, akt1, cngc1 and cngc4.
9.3	99.1	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.154 1 GO:0006694 The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
0.143 1 GO:0016132 The chemical reactions and pathways resulting in the formation of brassinosteroids, any of a group of steroid derivatives that occur at very low concentrations in plant tissues and may have hormone-like effects.
0.057 1 GO:0009911 Any process that activates or increases the frequency, rate or extent of flower development.

SF	Genes	GO ID	Process Name
0.154	1	GO:0006694	The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
0.143	1	GO:0016132	The chemical reactions and pathways resulting in the formation of brassinosteroids, any of a group of steroid derivatives that occur at very low concentrations in plant tissues and may have hormone-like effects.
0.057	1	GO:0009911	Any process that activates or increases the frequency, rate or extent of flower development.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.065 1 00100 Steroid biosynthesis
0.013 1 01066 Biosynthesis of alkaloids derived from terpenoid and polyketide
0.010 1 01062 Biosynthesis of terpenoids and steroids

SF	Genes	KEGG ID	Pathway name
0.065	1	00100	Steroid biosynthesis
0.013	1	01066	Biosynthesis of alkaloids derived from terpenoid and polyketide
0.010	1	01062	Biosynthesis of terpenoids and steroids

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	At5g62690
Gene name	TUB2
Module size	5 genes
NF	0.17
%ile	14.5

Co-expression analysis

Gene ID At5g62690 Gene name TUB2 Module size 5 genes NF 0.17 %ile 14.5

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 KEGG0.065100100Steroid biosynthesis0.013101066Biosynthesis of alkaloids derived from terpenoid and polyketide0.010101062Biosynthesis of terpenoids and steroids

Inter-species module comparison

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

Gene ID At5g62690

Gene name TUB2

Module size 5 genes

NF 0.17

%ile 14.5

: 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
0.065 1 00100 Steroid biosynthesis
0.013 1 01066 Biosynthesis of alkaloids derived from terpenoid and polyketide
0.010 1 01062 Biosynthesis of terpenoids and steroids

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