CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At4g36110

Gene name auxin-responsive protein, putative

Module size 8 genes

NF 0.01

%ile 0.2

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 At4g36110 829768 auxin-responsive protein, putative F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO O.I. H.G. S.X.
0.08 2.3 0.60 At5g16440 831505 IPP1 (ISOPENTENYL DIPHOSPHATE ISOMERASE 1) Encodes a protein with isopentenyl diphosphate:dimethylallyl diphosphate isomerase activity. There is genetic evidence that it functions in the mevalonate, but not the MEP biosynthetic pathway. O.I. H.G. S.X.
0.04 0.9 0.60 At3g60520 825223 unknown protein F:unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.01 0.2 0.64 At1g18400 838421 BEE1 (BR Enhanced Expression 1) F:transcription factor activity;P:regulation of transcription;C:nucleus;PFMO O.I. H.G. S.X.
0.01 0.2 0.60 At1g27930 839686 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POB O.I. H.G. S.X.
- 0.0 0.61 At4g09460 826530 ATMYB6 Encodes myb6 DNA-binding protein. O.I. H.G. S.X.
- 0.0 0.61 At4g14560 827103 IAA1 (INDOLE-3-ACETIC ACID INDUCIBLE) auxin (indole-3-acetic acid) induced gene (IAA1) encoding a short-lived nuclear-localized transcriptional regulator protein. O.I. H.G. S.X.
- 0.0 0.63 At4g16360 827331 AMP-activated protein kinase F:AMP-activated protein kinase activity;P:N-terminal protein myristoylation;C:chloroplast;MFPOB 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	At4g36110	829768	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	H.G.	S.X.
0.08	2.3	0.60	At5g16440	831505	IPP1 (ISOPENTENYL DIPHOSPHATE ISOMERASE 1)	Encodes a protein with isopentenyl diphosphate:dimethylallyl diphosphate isomerase activity. There is genetic evidence that it functions in the mevalonate, but not the MEP biosynthetic pathway.	O.I.	H.G.	S.X.
0.04	0.9	0.60	At3g60520	825223	unknown protein	F:unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.01	0.2	0.64	At1g18400	838421	BEE1 (BR Enhanced Expression 1)	F:transcription factor activity;P:regulation of transcription;C:nucleus;PFMO	O.I.	H.G.	S.X.
0.01	0.2	0.60	At1g27930	839686	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POB	O.I.	H.G.	S.X.
-	0.0	0.61	At4g09460	826530	ATMYB6	Encodes myb6 DNA-binding protein.	O.I.	H.G.	S.X.
-	0.0	0.61	At4g14560	827103	IAA1 (INDOLE-3-ACETIC ACID INDUCIBLE)	auxin (indole-3-acetic acid) induced gene (IAA1) encoding a short-lived nuclear-localized transcriptional regulator protein.	O.I.	H.G.	S.X.
-	0.0	0.63	At4g16360	827331	AMP-activated protein kinase	F:AMP-activated protein kinase activity;P:N-terminal protein myristoylation;C:chloroplast;MFPOB	O.I.	H.G.	S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.17	10.2	0.57	At2g18010	816313	auxin-responsive family protein	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	H.G.	S.X.
0.12	4.9	0.56	At1g65445	842856	transferase-related	F:transferase activity, transferring acyl groups other than amino-acyl groups;P:biological_process unknown;C:cellular_component unknown;PF	O.I.	H.G.	S.X.
0.09	2.8	0.54	At3g01980	821069	short-chain dehydrogenase/reductase (SDR) family protein	F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:peroxisome;BOFMPA	O.I.	H.G.	S.X.
0.09	2.8	0.54	At4g34770	829629	auxin-responsive family protein	F:unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	H.G.	S.X.
0.08	2.3	0.59	At3g14380	820659	integral membrane family protein	F:unknown;P:unknown;C:membrane;P	O.I.	H.G.	S.X.
0.07	1.9	0.54	At3g55290	824695	short-chain dehydrogenase/reductase (SDR) family protein	F:oxidoreductase activity, binding, catalytic activity;P:metabolic process;C:peroxisome;BOMFPAV	O.I.	H.G.	S.X.
0.06	1.4	0.55	At3g03830	821123	auxin-responsive protein, putative	F:molecular_function unknown;P:response to auxin stimulus;C:unknown;PO	O.I.	H.G.	S.X.
0.06	1.4	0.54	At1g02470	837812	-	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;BOP	O.I.	H.G.	S.X.
0.06	1.4	0.55	At1g65450	842857	transferase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PF	O.I.	H.G.	S.X.
0.05	1.1	0.56	At2g42900	818891	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PM	O.I.	H.G.	S.X.

Link to AtGenExpress Visualization Tool

Specific experiments for the module

Std2 GX %ile GSM ID Assay name GSE ID Experiment title Link to GEO
222.4 100.0 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
166.5 100.0 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
40.2 99.8 GSM205156 protoplast_controlDNA_rep1 GSE8257 Identification of KIN10-target genes in Arabidopsis mesophyll cells
32.7 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
24.8 99.6 GSM205160 protoplast_controlDNA_rep2 GSE8257 Identification of KIN10-target genes in Arabidopsis mesophyll cells
21.8 99.6 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.8 99.6 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
19.9 99.6 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.8 99.6 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
19.1 99.6 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
19.1 99.6 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.7 99.5 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.7 99.5 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.6 99.5 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.1 99.5 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.0 99.5 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.0 99.5 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.8 99.5 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.3 99.5 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.0 99.5 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.7 99.5 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.4 99.5 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.9 99.5 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.2 99.4 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.2 99.4 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.4 99.3 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.8 99.2 GSM133126 S0_2H_B GSE5688 AtGenExpress: Response to sulfate limitation
10.5 99.2 GSM142906 WW002_ATH1_A2-willa-ISOX-REP2 GSE6181 Assembly of the cell wall pectic matrix.
9.9 99.1 GSM142907 WW002_ATH1_A2-willa-ISOX-REP3 GSE6181 Assembly of the cell wall pectic matrix.
9.8 99.1 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
9.1 99.1 GSM142905 WW002_ATH1_A1-willa-CON-REP3 GSE6181 Assembly of the cell wall pectic matrix.

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
222.4	100.0	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
166.5	100.0	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
40.2	99.8	GSM205156	protoplast_controlDNA_rep1	GSE8257	Identification of KIN10-target genes in Arabidopsis mesophyll cells
32.7	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
24.8	99.6	GSM205160	protoplast_controlDNA_rep2	GSE8257	Identification of KIN10-target genes in Arabidopsis mesophyll cells
21.8	99.6	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.8	99.6	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
19.9	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.8	99.6	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.1	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.1	99.6	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.7	99.5	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.7	99.5	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.6	99.5	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.1	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.0	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.0	99.5	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.8	99.5	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.3	99.5	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.0	99.5	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.7	99.5	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.4	99.5	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.9	99.5	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.2	99.4	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.2	99.4	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.4	99.3	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.8	99.2	GSM133126	S0_2H_B	GSE5688	AtGenExpress: Response to sulfate limitation
10.5	99.2	GSM142906	WW002_ATH1_A2-willa-ISOX-REP2	GSE6181	Assembly of the cell wall pectic matrix.
9.9	99.1	GSM142907	WW002_ATH1_A2-willa-ISOX-REP3	GSE6181	Assembly of the cell wall pectic matrix.
9.8	99.1	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
9.1	99.1	GSM142905	WW002_ATH1_A1-willa-CON-REP3	GSE6181	Assembly of the cell wall pectic matrix.

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.222 1 GO:0009240 The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids.
0.069 1 GO:0008299 The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
0.059 1 GO:0015995 The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors.

SF	Genes	GO ID	Process Name
0.222	1	GO:0009240	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate, an isomer of dimethylallyl diphosphate and the key precursor of all isoprenoids.
0.069	1	GO:0008299	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
0.059	1	GO:0015995	The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.041 1 00900 Terpenoid backbone biosynthesis
0.012 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
0.041	1	00900	Terpenoid backbone biosynthesis
0.012	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

Back to the KAGIANA project homepage

Gene ID	At4g36110
Gene name	auxin-responsive protein, putative
Module size	8 genes
NF	0.01
%ile	0.2

Co-expression analysis

Gene ID At4g36110 Gene name auxin-responsive protein, putative Module size 8 genes NF 0.01 %ile 0.2

Co-expression network

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein: VF over 0.50, : over 0.25, : below 0.25

Co-expressed 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 KEGG0.041100900Terpenoid backbone biosynthesis0.012101066Biosynthesis 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 At4g36110

Gene name auxin-responsive protein, putative

Module size 8 genes

NF 0.01

%ile 0.2

: 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
0.041 1 00900 Terpenoid backbone biosynthesis
0.012 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