CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g58870

Gene name ftsh9 (FtsH protease 9)

Module size 5 genes

NF 0.54

%ile 75.2

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
0.43 55.3 1.00 At5g58870 836004 ftsh9 (FtsH protease 9) encodes an FtsH protease that is localized to the chloroplast O.I. H.G. S.X.
0.67 81.6 0.93 At5g64840 836607 ATGCN5 (A. THALIANA GENERAL CONTROL NON-REPRESSIBLE 5) member of GCN subfamily O.I. H.G. S.X.
0.60 75.7 0.92 At5g67030 836838 ABA1 (ABA DEFICIENT 1) Encodes a single copy zeaxanthin epoxidase gene that functions in first step of the biosynthesis of the abiotic stress hormone abscisic acid (ABA). Mutants in this gene are unable to express female sterility in response to beta-aminobutyric acid, as wild type plants do. O.I. H.G. S.X.
0.55 70.6 0.92 At1g66330 842950 senescence-associated family protein F:unknown;P:senescence;C:unknown;PB O.I. H.G. S.X.
0.40 50.8 0.90 At3g01060 821278 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;BOFP O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.43	55.3	1.00	At5g58870	836004	ftsh9 (FtsH protease 9)	encodes an FtsH protease that is localized to the chloroplast	O.I.	H.G.	S.X.
0.67	81.6	0.93	At5g64840	836607	ATGCN5 (A. THALIANA GENERAL CONTROL NON-REPRESSIBLE 5)	member of GCN subfamily	O.I.	H.G.	S.X.
0.60	75.7	0.92	At5g67030	836838	ABA1 (ABA DEFICIENT 1)	Encodes a single copy zeaxanthin epoxidase gene that functions in first step of the biosynthesis of the abiotic stress hormone abscisic acid (ABA). Mutants in this gene are unable to express female sterility in response to beta-aminobutyric acid, as wild type plants do.	O.I.	H.G.	S.X.
0.55	70.6	0.92	At1g66330	842950	senescence-associated family protein	F:unknown;P:senescence;C:unknown;PB	O.I.	H.G.	S.X.
0.40	50.8	0.90	At3g01060	821278	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;BOFP	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
179.6 100.0 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
118.3 99.9 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
84.6 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
78.9 99.9 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
77.6 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
73.9 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.4 99.9 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.4 99.9 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.4 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
68.2 99.9 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.0 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
64.9 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
61.4 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.8 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.6 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.8 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.4 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.0 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.0 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
47.5 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.9 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.2 99.7 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
20.9 99.6 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.8 99.5 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
15.3 99.4 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
13.9 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
13.6 99.4 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
13.1 99.4 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
12.6 99.3 GSM131106 Broadley_1-4_A4-Bo-P3-phosphate-starved_Rep3_ATH1 GSE5614 Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)
12.5 99.3 GSM134206 Murray_3-3_D5-GROWTH_Rep1_ATH1 GSE5750 Growth of suspension-cultured cells
11.5 99.3 GSM176880 AWP_Control_2 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
11.1 99.2 GSM134208 Murray_3-4_D7-GROWTH_Rep1_ATH1 GSE5750 Growth of suspension-cultured cells
10.4 99.2 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
179.6	100.0	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
118.3	99.9	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
84.6	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
78.9	99.9	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
77.6	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
73.9	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.4	99.9	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.4	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.4	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
68.2	99.9	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
66.0	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
64.9	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
61.4	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
59.8	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.6	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.8	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.4	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.0	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.0	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
47.5	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.9	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.2	99.7	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
20.9	99.6	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.8	99.5	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
15.3	99.4	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
13.9	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
13.6	99.4	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
13.1	99.4	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
12.6	99.3	GSM131106	Broadley_1-4_A4-Bo-P3-phosphate-starved_Rep3_ATH1	GSE5614	Changes in Gene Expression in Brassica oleracea Shoots during Phosphate Starvation (Cross-species study)
12.5	99.3	GSM134206	Murray_3-3_D5-GROWTH_Rep1_ATH1	GSE5750	Growth of suspension-cultured cells
11.5	99.3	GSM176880	AWP_Control_2	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
11.1	99.2	GSM134208	Murray_3-4_D7-GROWTH_Rep1_ATH1	GSE5750	Growth of suspension-cultured cells
10.4	99.2	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.182 1 GO:0016123 The chemical reactions and pathways resulting in the formation of xanthophylls, oxygen-containing carotenoids.
0.154 1 GO:0010149 A preprogrammed process associated with the dismantling of an anatomical structure and an overall decline in metabolism. This may include the breakdown of organelles, membranes and other cellular components. An example of this process is found in Arabidopsis thaliana, when older leaves or floral organs are shed.
0.118 1 GO:0009688 The chemical reactions and pathways resulting in the formation of abscisic acid, 5-(1-hydroxy-2,6,6,trimethyl-4-oxocyclohex-2-en-1-y1)-3-methylpenta-2,4-dienoic acid.

SF	Genes	GO ID	Process Name
0.182	1	GO:0016123	The chemical reactions and pathways resulting in the formation of xanthophylls, oxygen-containing carotenoids.
0.154	1	GO:0010149	A preprogrammed process associated with the dismantling of an anatomical structure and an overall decline in metabolism. This may include the breakdown of organelles, membranes and other cellular components. An example of this process is found in Arabidopsis thaliana, when older leaves or floral organs are shed.
0.118	1	GO:0009688	The chemical reactions and pathways resulting in the formation of abscisic acid, 5-(1-hydroxy-2,6,6,trimethyl-4-oxocyclohex-2-en-1-y1)-3-methylpenta-2,4-dienoic acid.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.074 1 00906 Carotenoid biosynthesis
0.010 1 01062 Biosynthesis of terpenoids and steroids
0.006 1 01070 Biosynthesis of plant hormones

SF	Genes	KEGG ID	Pathway name
0.074	1	00906	Carotenoid biosynthesis
0.010	1	01062	Biosynthesis of terpenoids and steroids
0.006	1	01070	Biosynthesis of plant hormones

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	At5g58870
Gene name	ftsh9 (FtsH protease 9)
Module size	5 genes
NF	0.54
%ile	75.2

Co-expression analysis

Gene ID At5g58870 Gene name ftsh9 (FtsH protease 9) Module size 5 genes NF 0.54 %ile 75.2

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 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 KEGG0.074100906Carotenoid biosynthesis0.010101062Biosynthesis of terpenoids and steroids0.006101070Biosynthesis of plant hormones

Inter-species module comparison

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

Gene ID At5g58870

Gene name ftsh9 (FtsH protease 9)

Module size 5 genes

NF 0.54

%ile 75.2

: 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
0.074 1 00906 Carotenoid biosynthesis
0.010 1 01062 Biosynthesis of terpenoids and steroids
0.006 1 01070 Biosynthesis of plant hormones

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