CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g52320

Gene name CYP96A4

Module size 5 genes

NF 0.14

%ile 10.0

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
0.27 26.2 1.00 At5g52320 835308 CYP96A4 member of CYP96A O.I. H.G. S.X.
0.40 50.8 0.72 At1g19670 838554 ATCLH1 (ARABIDOPSIS THALIANA CORONATINE-INDUCED PROTEIN 1) Chlorophyllase is the first enzyme involved in chlorophyll degradation. It catalyzes the hydrolysis of the ester bond to yield chlorophyllide and phytol. AtCLH1 lacks a typical signal sequence for the chloroplast. Its expression is induced rapidly by methyljasmonate, a known promoter of senescence and chlorophyll degradation. O.I. H.G. S.X.
0.40 50.8 0.72 At3g25760 822167 AOC1 (ALLENE OXIDE CYCLASE 1) encodes allene oxide cyclase. One of four genes in Arabidopsis that encode this enzyme, which catalyzes an essential step in jasmonic acid biosynthesis. Gene expression is induced during senescence, a process that involves jasmonic acid signalling pathway. O.I. H.G. S.X.
0.40 50.8 0.70 At5g42650 834273 AOS (ALLENE OXIDE SYNTHASE) Encodes a member of the cytochrome p450 CYP74 gene family that functions as an allene oxide synthase. This enzyme catalyzes dehydration of the hydroperoxide to an unstable allene oxide in the JA biosynthetic pathway. It shows a dual catalytic activity, the major one being a 13-AOS but also expressing a 9-AOS activity. O.I. H.G. S.X.
0.03 0.6 0.70 At2g32290 817789 BAM6 (BETA-AMYLASE 6) F:cation binding, beta-amylase activity, catalytic activity;P:cellulose biosynthetic process, carbohydrate metabolic process, polysaccharide catabolic process;C:chloroplast;PBO O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.27	26.2	1.00	At5g52320	835308	CYP96A4	member of CYP96A	O.I.	H.G.	S.X.
0.40	50.8	0.72	At1g19670	838554	ATCLH1 (ARABIDOPSIS THALIANA CORONATINE-INDUCED PROTEIN 1)	Chlorophyllase is the first enzyme involved in chlorophyll degradation. It catalyzes the hydrolysis of the ester bond to yield chlorophyllide and phytol. AtCLH1 lacks a typical signal sequence for the chloroplast. Its expression is induced rapidly by methyljasmonate, a known promoter of senescence and chlorophyll degradation.	O.I.	H.G.	S.X.
0.40	50.8	0.72	At3g25760	822167	AOC1 (ALLENE OXIDE CYCLASE 1)	encodes allene oxide cyclase. One of four genes in Arabidopsis that encode this enzyme, which catalyzes an essential step in jasmonic acid biosynthesis. Gene expression is induced during senescence, a process that involves jasmonic acid signalling pathway.	O.I.	H.G.	S.X.
0.40	50.8	0.70	At5g42650	834273	AOS (ALLENE OXIDE SYNTHASE)	Encodes a member of the cytochrome p450 CYP74 gene family that functions as an allene oxide synthase. This enzyme catalyzes dehydration of the hydroperoxide to an unstable allene oxide in the JA biosynthetic pathway. It shows a dual catalytic activity, the major one being a 13-AOS but also expressing a 9-AOS activity.	O.I.	H.G.	S.X.
0.03	0.6	0.70	At2g32290	817789	BAM6 (BETA-AMYLASE 6)	F:cation binding, beta-amylase activity, catalytic activity;P:cellulose biosynthetic process, carbohydrate metabolic process, polysaccharide catabolic process;C:chloroplast;PBO	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
281.2 100.0 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
177.4 100.0 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
123.0 99.9 E-ATMX-35-raw-cel-1574334816
115.0 99.9 E-ATMX-35-raw-cel-1574334832
53.4 99.8 E-ATMX-35-raw-cel-1574334800
45.7 99.8 GSM131703 ATGE_83_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
41.0 99.8 GSM131707 ATGE_84_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
39.5 99.8 GSM131706 ATGE_84_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
39.3 99.8 GSM131705 ATGE_83_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
38.8 99.8 GSM131708 ATGE_84_D GSE5634 AtGenExpress: Developmental series (siliques and seeds)
37.2 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.6 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
35.2 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.7 99.7 GSM131704 ATGE_83_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
31.7 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.2 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.3 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.9 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.8 99.7 GSM131702 ATGE_82_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
27.7 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.1 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.6 99.7 GSM131700 ATGE_82_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
26.5 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.7 99.6 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.6 99.6 GSM131701 ATGE_82_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
24.4 99.6 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.1 99.6 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.8 99.6 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
20.5 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
20.1 99.6 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
18.3 99.5 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.9 99.5 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.0 99.5 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.2 99.4 GSM131698 ATGE_81_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
15.2 99.4 GSM131699 ATGE_81_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
14.7 99.4 GSM131696 ATGE_79_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
14.7 99.4 GSM131697 ATGE_81_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
13.9 99.4 GSM131694 ATGE_79_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
13.6 99.4 GSM176879 AWP_Control_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
12.8 99.3 GSM131695 ATGE_79_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
11.9 99.3 GSM10453 WT Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
11.8 99.3 GSM10451 WT Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
11.1 99.2 GSM10454 WT Post-Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
9.9 99.1 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.4 99.1 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.3 99.1 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.2 99.1 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
281.2	100.0	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
177.4	100.0	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
123.0	99.9	E-ATMX-35-raw-cel-1574334816
115.0	99.9	E-ATMX-35-raw-cel-1574334832
53.4	99.8	E-ATMX-35-raw-cel-1574334800
45.7	99.8	GSM131703	ATGE_83_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
41.0	99.8	GSM131707	ATGE_84_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
39.5	99.8	GSM131706	ATGE_84_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
39.3	99.8	GSM131705	ATGE_83_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
38.8	99.8	GSM131708	ATGE_84_D	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
37.2	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.6	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
35.2	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.7	99.7	GSM131704	ATGE_83_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
31.7	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.2	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
29.3	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.9	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.8	99.7	GSM131702	ATGE_82_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
27.7	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.1	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.6	99.7	GSM131700	ATGE_82_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
26.5	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.7	99.6	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.6	99.6	GSM131701	ATGE_82_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
24.4	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.1	99.6	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.8	99.6	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
20.5	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
20.1	99.6	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
18.3	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.9	99.5	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.0	99.5	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.2	99.4	GSM131698	ATGE_81_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.2	99.4	GSM131699	ATGE_81_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
14.7	99.4	GSM131696	ATGE_79_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
14.7	99.4	GSM131697	ATGE_81_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
13.9	99.4	GSM131694	ATGE_79_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
13.6	99.4	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
12.8	99.3	GSM131695	ATGE_79_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
11.9	99.3	GSM10453	WT Mature Green Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
11.8	99.3	GSM10451	WT Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
11.1	99.2	GSM10454	WT Post-Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
9.9	99.1	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.4	99.1	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.3	99.1	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.2	99.1	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.333 1 GO:0019373
0.250 1 GO:0031407 The chemical reactions and pathways involving any oxylipin, any of a group of biologically active compounds formed by oxidative metabolism of polyunsaturated fatty acids.
0.200 1 GO:0000272 The chemical reactions and pathways resulting in the breakdown of polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages.

SF	Genes	GO ID	Process Name
0.333	1	GO:0019373
0.250	1	GO:0031407	The chemical reactions and pathways involving any oxylipin, any of a group of biologically active compounds formed by oxidative metabolism of polyunsaturated fatty acids.
0.200	1	GO:0000272	The chemical reactions and pathways resulting in the breakdown of polysaccharides, polymers of more than 10 monosaccharide residues joined by glycosidic linkages.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.118 2 00592 alpha-Linolenic acid metabolism
0.065 1 00860 Porphyrin and chlorophyll metabolism
0.028 1 00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis

SF	Genes	KEGG ID	Pathway name
0.118	2	00592	alpha-Linolenic acid metabolism
0.065	1	00860	Porphyrin and chlorophyll metabolism
0.028	1	00945	Stilbenoid, diarylheptanoid and gingerol biosynthesis

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	At5g52320
Gene name	CYP96A4
Module size	5 genes
NF	0.14
%ile	10.0

Co-expression analysis

Gene ID At5g52320 Gene name CYP96A4 Module size 5 genes NF 0.14 %ile 10.0

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 KEGG0.118200592alpha-Linolenic acid metabolism0.065100860Porphyrin and chlorophyll metabolism0.028100945Stilbenoid, diarylheptanoid and gingerol biosynthesis

Inter-species module comparison

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

Gene ID At5g52320

Gene name CYP96A4

Module size 5 genes

NF 0.14

%ile 10.0

: 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
0.118 2 00592 alpha-Linolenic acid metabolism
0.065 1 00860 Porphyrin and chlorophyll metabolism
0.028 1 00945 Stilbenoid, diarylheptanoid and gingerol biosynthesis

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