CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g29690

Gene name CAD1 (constitutively activated cell death 1)

Module size 6 genes

NF 0.67

%ile 86.9

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 At1g29690 839846 CAD1 (constitutively activated cell death 1) Encodes a protein containing a domain with significant homology to the MACPF (membrane attack complex and perforin) domain of complements and perforin proteins that are involved in innate immunity in animals. Transgenic cad1-1 mutant plants show lesions seen in the hypersensitive response, as well as a spontaneous activation of expression of pathogenesis-related genes and leading to a 32-fold increase in salicylic acid (SA). CAD1 is postulated to act as a negative regulator controlling SA-mediated pathway of programmed cell death in plant immunity. O.I. H.G. S.X.
0.80 89.8 0.88 At4g39640 830118 GGT1 (GAMMA-GLUTAMYL TRANSPEPTIDASE 1) The gene encodes a gamma-glutamyltransferase (AKA gamma-glutamyl transpeptidase, EC 2.3.2.2) that is located in vascular tissues (predominantly phloem) of leaves and is involved in the degradation of glutathione. The encoded enzyme also mitigates oxidative stress by metabolizing GSSG (oxidized form of GSH - glutathione) in the apoplast. O.I. H.G. S.X.
0.73 85.5 0.90 At4g34150 829563 C2 domain-containing protein F:unknown;P:response to cold;C:unknown;MPFOBVA O.I. H.G. S.X.
0.71 84.2 0.93 At1g28380 839735 NSL1 (necrotic spotted lesions 1) This gene is predicted to encode a protein involved in negatively regulating salicylic acid-related defense responses and cell death programs. nsl1 mutants develop necrotic lesions spontaneously and show other features of a defense response, such as higher levels of SA and disease resistance-related transcripts, in the absence of a biotic stimulus. The NSL1 protein is predicted to have a MACPF domain, found in proteins that form a transmembrane pore in mammalian immune responses. NSL1 transcript levels do not appear to change in response to biotic stresses, but are elevated by cycloheximide in seedlings, and by sodium chloride in roots. O.I. H.G. S.X.
0.67 81.6 0.89 At3g09830 820141 protein kinase, putative F:protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA O.I. H.G. S.X.
0.55 70.6 0.87 At3g45640 823706 ATMPK3 (ARABIDOPSIS THALIANA MITOGEN-ACTIVATED PROTEIN KINASE 3) Encodes a mitogen-activated kinase whose mRNA levels increase in response to touch, cold, salinity stress and chitin oligomers.Also functions in ovule development. Heterozygous MPK3 mutants in a homozygous MPK6 background are female sterile due to defects in integument development. MPK3 can be dephosphorylated by MKP2 in vitro. 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	At1g29690	839846	CAD1 (constitutively activated cell death 1)	Encodes a protein containing a domain with significant homology to the MACPF (membrane attack complex and perforin) domain of complements and perforin proteins that are involved in innate immunity in animals. Transgenic cad1-1 mutant plants show lesions seen in the hypersensitive response, as well as a spontaneous activation of expression of pathogenesis-related genes and leading to a 32-fold increase in salicylic acid (SA). CAD1 is postulated to act as a negative regulator controlling SA-mediated pathway of programmed cell death in plant immunity.	O.I.	H.G.	S.X.
0.80	89.8	0.88	At4g39640	830118	GGT1 (GAMMA-GLUTAMYL TRANSPEPTIDASE 1)	The gene encodes a gamma-glutamyltransferase (AKA gamma-glutamyl transpeptidase, EC 2.3.2.2) that is located in vascular tissues (predominantly phloem) of leaves and is involved in the degradation of glutathione. The encoded enzyme also mitigates oxidative stress by metabolizing GSSG (oxidized form of GSH - glutathione) in the apoplast.	O.I.	H.G.	S.X.
0.73	85.5	0.90	At4g34150	829563	C2 domain-containing protein	F:unknown;P:response to cold;C:unknown;MPFOBVA	O.I.	H.G.	S.X.
0.71	84.2	0.93	At1g28380	839735	NSL1 (necrotic spotted lesions 1)	This gene is predicted to encode a protein involved in negatively regulating salicylic acid-related defense responses and cell death programs. nsl1 mutants develop necrotic lesions spontaneously and show other features of a defense response, such as higher levels of SA and disease resistance-related transcripts, in the absence of a biotic stimulus. The NSL1 protein is predicted to have a MACPF domain, found in proteins that form a transmembrane pore in mammalian immune responses. NSL1 transcript levels do not appear to change in response to biotic stresses, but are elevated by cycloheximide in seedlings, and by sodium chloride in roots.	O.I.	H.G.	S.X.
0.67	81.6	0.89	At3g09830	820141	protein kinase, putative	F:protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA	O.I.	H.G.	S.X.
0.55	70.6	0.87	At3g45640	823706	ATMPK3 (ARABIDOPSIS THALIANA MITOGEN-ACTIVATED PROTEIN KINASE 3)	Encodes a mitogen-activated kinase whose mRNA levels increase in response to touch, cold, salinity stress and chitin oligomers.Also functions in ovule development. Heterozygous MPK3 mutants in a homozygous MPK6 background are female sterile due to defects in integument development. MPK3 can be dephosphorylated by MKP2 in vitro.	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
214.7 100.0 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
145.8 99.9 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
39.8 99.8 GSM10454 WT Post-Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
32.0 99.7 GSM10456 WT Post-Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
20.3 99.6 GSM131701 ATGE_82_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
20.0 99.6 GSM131706 ATGE_84_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
19.8 99.6 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
19.4 99.6 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.3 99.5 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.8 99.5 GSM131702 ATGE_82_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
15.6 99.5 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.5 99.5 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.9 99.4 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.7 99.4 GSM131707 ATGE_84_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
14.5 99.4 GSM142649 MC002_ATH1_A9.3-dubos-aah GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.2 99.4 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.8 99.3 GSM142647 MC002_ATH1_A9.1-dubos-aah GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.5 99.3 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.4 99.3 GSM131708 ATGE_84_D GSE5634 AtGenExpress: Developmental series (siliques and seeds)
12.1 99.3 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.0 99.3 GSM142648 MC002_ATH1_A9.2-dubos-aah GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.4 99.3 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.3 99.3 GSM131700 ATGE_82_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
11.0 99.2 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.8 99.2 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.7 99.2 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.9 99.1 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.8 99.1 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.8 99.1 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.8 99.1 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7 99.1 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 GSM10451 WT Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
9.2 99.1 GSM142653 MC002_ATH1_A11.1-dubos-mxh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.9 99.0 GSM142655 MC002_ATH1_A11.3-dubos-mxh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.7 99.0 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
214.7	100.0	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
145.8	99.9	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
39.8	99.8	GSM10454	WT Post-Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
32.0	99.7	GSM10456	WT Post-Mature Green Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
20.3	99.6	GSM131701	ATGE_82_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
20.0	99.6	GSM131706	ATGE_84_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
19.8	99.6	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
19.4	99.6	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.3	99.5	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.8	99.5	GSM131702	ATGE_82_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.6	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.5	99.5	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.9	99.4	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.7	99.4	GSM131707	ATGE_84_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
14.5	99.4	GSM142649	MC002_ATH1_A9.3-dubos-aah	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
13.2	99.4	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.8	99.3	GSM142647	MC002_ATH1_A9.1-dubos-aah	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.5	99.3	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.4	99.3	GSM131708	ATGE_84_D	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
12.1	99.3	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.0	99.3	GSM142648	MC002_ATH1_A9.2-dubos-aah	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.4	99.3	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.3	99.3	GSM131700	ATGE_82_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
11.0	99.2	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.8	99.2	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.7	99.2	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.9	99.1	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.8	99.1	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.8	99.1	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.8	99.1	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7	99.1	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4	99.1	GSM10451	WT Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
9.2	99.1	GSM142653	MC002_ATH1_A11.1-dubos-mxh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.9	99.0	GSM142655	MC002_ATH1_A11.3-dubos-mxh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.7	99.0	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, 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
0.286 1 GO:0000169 Any process that initiates the activity of the inactive enzyme MAP kinase activity during osmolarity sensing.
0.250 1 GO:0080136 The process that enables cells to respond in a more rapid and robust manner than nonprimed cells to much lower levels of a stimulus indicating the organism is under stress.
0.222 1 GO:0052542 Any process by which callose is transported to, and/or maintained in, a specific location during the defense response. Callose is a linear 1,3-beta-d-glucan formed from UDP-glucose and is found in certain plant cell walls.

SF	Genes	GO ID	Process Name
0.286	1	GO:0000169	Any process that initiates the activity of the inactive enzyme MAP kinase activity during osmolarity sensing.
0.250	1	GO:0080136	The process that enables cells to respond in a more rapid and robust manner than nonprimed cells to much lower levels of a stimulus indicating the organism is under stress.
0.222	1	GO:0052542	Any process by which callose is transported to, and/or maintained in, a specific location during the defense response. Callose is a linear 1,3-beta-d-glucan formed from UDP-glucose and is found in certain plant cell walls.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.200 1 00430 Taurine and hypotaurine metabolism
0.133 1 00590 Arachidonic acid metabolism
0.091 1 04650 Natural killer cell mediated cytotoxicity

SF	Genes	KEGG ID	Pathway name
0.200	1	00430	Taurine and hypotaurine metabolism
0.133	1	00590	Arachidonic acid metabolism
0.091	1	04650	Natural killer cell mediated cytotoxicity

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	At1g29690
Gene name	CAD1 (constitutively activated cell death 1)
Module size	6 genes
NF	0.67
%ile	86.9

Co-expression analysis

Gene ID At1g29690 Gene name CAD1 (constitutively activated cell death 1) Module size 6 genes NF 0.67 %ile 86.9

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 KEGG0.200100430Taurine and hypotaurine metabolism0.133100590Arachidonic acid metabolism0.091104650Natural killer cell mediated cytotoxicity

Inter-species module comparison

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

Gene ID At1g29690

Gene name CAD1 (constitutively activated cell death 1)

Module size 6 genes

NF 0.67

%ile 86.9

: 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
0.200 1 00430 Taurine and hypotaurine metabolism
0.133 1 00590 Arachidonic acid metabolism
0.091 1 04650 Natural killer cell mediated cytotoxicity

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