CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g21430

Gene name -

Module size 5 genes

NF 0.84

%ile 96.0

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
0.60 75.7 1.00 At3g21430 821697 - - O.I. H.G. S.X.
1.00 100.0 0.91 At5g44150 834438 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMBO O.I. H.G. S.X.
0.89 94.6 0.86 At2g20710 816599 pentatricopeptide (PPR) repeat-containing protein F:unknown;P:biological_process unknown;C:mitochondrion;POFMB O.I. H.G. S.X.
0.89 94.6 0.87 At3g49710 824133 pentatricopeptide (PPR) repeat-containing protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFB O.I. H.G. S.X.
0.86 93.1 0.80 At2g07696 815372 ribosomal protein S7 family protein F:structural constituent of ribosome;P:translation;C:ribosome, small ribosomal subunit, intracellular;BOPMAF O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.60	75.7	1.00	At3g21430	821697	-	-	O.I.	H.G.	S.X.
1.00	100.0	0.91	At5g44150	834438	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;PMBO	O.I.	H.G.	S.X.
0.89	94.6	0.86	At2g20710	816599	pentatricopeptide (PPR) repeat-containing protein	F:unknown;P:biological_process unknown;C:mitochondrion;POFMB	O.I.	H.G.	S.X.
0.89	94.6	0.87	At3g49710	824133	pentatricopeptide (PPR) repeat-containing protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POMFB	O.I.	H.G.	S.X.
0.86	93.1	0.80	At2g07696	815372	ribosomal protein S7 family protein	F:structural constituent of ribosome;P:translation;C:ribosome, small ribosomal subunit, intracellular;BOPMAF	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
111.2 99.9 GSM216981 Vector_shoots_4h_GA4+DEX_repl2 GSE8741 DELLA protein direct targets in Arabidopsis
105.0 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
99.8 99.9 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
99.2 99.9 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
94.9 99.9 E-ATMX-35-raw-cel-1574334832
92.8 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
90.2 99.9 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
89.5 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
87.2 99.9 GSM216973 Vector_shoots_4h_GA4+DEX_repl1 GSE8741 DELLA protein direct targets in Arabidopsis
82.1 99.9 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
81.6 99.9 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
80.8 99.9 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
80.0 99.9 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
79.2 99.9 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
71.8 99.9 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.9 99.9 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.6 99.9 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
61.4 99.8 E-ATMX-35-raw-cel-1574334816
61.3 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.1 99.8 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
56.9 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
54.7 99.8 E-ATMX-35-raw-cel-1574334800
53.9 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.4 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.7 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
52.5 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.2 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.7 99.8 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
35.7 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.3 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.9 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
16.6 99.5 GSM133030 BC482-2 GSE5684 AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
14.4 99.4 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
14.3 99.4 GSM131160 AtGen_C-10_1-Pi-6_REP1_ATH1 GSE5616 AtGenExpress: Response to Phytophthora infestans
13.7 99.4 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.4 99.4 GSM131161 AtGen_C-11_2-Pi-6_REP2_ATH1 GSE5616 AtGenExpress: Response to Phytophthora infestans
12.4 99.3 E-MEXP-807-raw-cel-1173272977
11.9 99.3 GSM311274 Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
11.9 99.3 GSM133029 BC482-1 GSE5684 AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
11.8 99.3 GSM133120 RIKEN-YAMAUCHI2B GSE5687 AtGenExpress: Different temperature treatment of seeds
11.4 99.3 E-MEXP-849-raw-cel-1181981030
11.3 99.3 E-MEXP-1474-raw-cel-1593932609
11.2 99.2 GSM133025 BC181-1 GSE5684 AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
10.7 99.2 GSM133810 Diamond_A-3-Diamo-fum_SLD GSE5735 Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
10.5 99.2 GSM322554 genotype: ataf1-1 mutant, ecotype Col-0 - treated or untreated: Bgh inoculated - rep1 GSE12856 Penetration resistance: Wildtype and ataf1-1 mutant response to Bgh 12 h after inoculation, 22 factorial design
10.5 99.2 GSM131162 AtGen_C-12_3-Pi-6_REP3_ATH1 GSE5616 AtGenExpress: Response to Phytophthora infestans
9.8 99.1 E-MEXP-849-raw-cel-1181981046
9.4 99.1 E-MEXP-849-raw-cel-1181981006
9.2 99.1 GSM133119 RIKEN-YAMAUCHI2A GSE5687 AtGenExpress: Different temperature treatment of seeds
9.2 99.1 GSM322549 genotype: Wild-type Arabidopsis, ecotype Col-0 - treated or untreated: Bgh inoculated - rep2 GSE12856 Penetration resistance: Wildtype and ataf1-1 mutant response to Bgh 12 h after inoculation, 22 factorial design
9.2 99.1 GSM131167 AtGen_C-17_2-Pi-24_REP2_ATH1 GSE5616 AtGenExpress: Response to Phytophthora infestans
9.0 99.1 E-MEXP-509-raw-cel-829148456
9.0 99.1 GSM13783 Dexamethasone plus cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
8.8 99.0 E-MEXP-849-raw-cel-1181981022
8.8 99.0 GSM133811 Diamond_A-4-Diamo-fum_SLD GSE5735 Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
111.2	99.9	GSM216981	Vector_shoots_4h_GA4+DEX_repl2	GSE8741	DELLA protein direct targets in Arabidopsis
105.0	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
99.8	99.9	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
99.2	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
94.9	99.9	E-ATMX-35-raw-cel-1574334832
92.8	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
90.2	99.9	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
89.5	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
87.2	99.9	GSM216973	Vector_shoots_4h_GA4+DEX_repl1	GSE8741	DELLA protein direct targets in Arabidopsis
82.1	99.9	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
81.6	99.9	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
80.8	99.9	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
80.0	99.9	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
79.2	99.9	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
71.8	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.9	99.9	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.6	99.9	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
61.4	99.8	E-ATMX-35-raw-cel-1574334816
61.3	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.1	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
56.9	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
54.7	99.8	E-ATMX-35-raw-cel-1574334800
53.9	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.4	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.7	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.5	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.2	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.7	99.8	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
35.7	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.3	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.9	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
16.6	99.5	GSM133030	BC482-2	GSE5684	AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
14.4	99.4	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
14.3	99.4	GSM131160	AtGen_C-10_1-Pi-6_REP1_ATH1	GSE5616	AtGenExpress: Response to Phytophthora infestans
13.7	99.4	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.4	99.4	GSM131161	AtGen_C-11_2-Pi-6_REP2_ATH1	GSE5616	AtGenExpress: Response to Phytophthora infestans
12.4	99.3	E-MEXP-807-raw-cel-1173272977
11.9	99.3	GSM311274	Laser capture microdissected (LCM) embryo proper at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
11.9	99.3	GSM133029	BC482-1	GSE5684	AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
11.8	99.3	GSM133120	RIKEN-YAMAUCHI2B	GSE5687	AtGenExpress: Different temperature treatment of seeds
11.4	99.3	E-MEXP-849-raw-cel-1181981030
11.3	99.3	E-MEXP-1474-raw-cel-1593932609
11.2	99.2	GSM133025	BC181-1	GSE5684	AtGenExpress: Pathogen Series: Response to Botrytis cinerea infection
10.7	99.2	GSM133810	Diamond_A-3-Diamo-fum_SLD	GSE5735	Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
10.5	99.2	GSM322554	genotype: ataf1-1 mutant, ecotype Col-0 - treated or untreated: Bgh inoculated - rep1	GSE12856	Penetration resistance: Wildtype and ataf1-1 mutant response to Bgh 12 h after inoculation, 2*2 factorial design
10.5	99.2	GSM131162	AtGen_C-12_3-Pi-6_REP3_ATH1	GSE5616	AtGenExpress: Response to Phytophthora infestans
9.8	99.1	E-MEXP-849-raw-cel-1181981046
9.4	99.1	E-MEXP-849-raw-cel-1181981006
9.2	99.1	GSM133119	RIKEN-YAMAUCHI2A	GSE5687	AtGenExpress: Different temperature treatment of seeds
9.2	99.1	GSM322549	genotype: Wild-type Arabidopsis, ecotype Col-0 - treated or untreated: Bgh inoculated - rep2	GSE12856	Penetration resistance: Wildtype and ataf1-1 mutant response to Bgh 12 h after inoculation, 2*2 factorial design
9.2	99.1	GSM131167	AtGen_C-17_2-Pi-24_REP2_ATH1	GSE5616	AtGenExpress: Response to Phytophthora infestans
9.0	99.1	E-MEXP-509-raw-cel-829148456
9.0	99.1	GSM13783	Dexamethasone plus cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
8.8	99.0	E-MEXP-849-raw-cel-1181981022
8.8	99.0	GSM133811	Diamond_A-4-Diamo-fum_SLD	GSE5735	Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG

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	At3g21430
Gene name	-
Module size	5 genes
NF	0.84
%ile	96.0

Co-expression analysis

Gene ID At3g21430 Gene name - Module size 5 genes NF 0.84 %ile 96.0

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

SFGenesGO IDProcess NameLink to AmiGO

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG

Inter-species module comparison

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

Gene ID At3g21430

Gene name -

Module size 5 genes

NF 0.84

%ile 96.0

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

SF Genes GO ID Process Name Link to AmiGO

SF Genes KEGG ID Pathway name Link to KEGG

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