CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g29575

Gene name AFP3 (ABI FIVE BINDING PROTEIN 3)

Module size 7 genes

NF 0.15

%ile 12.2

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
0.60 75.7 1.00 At3g29575 822619 AFP3 (ABI FIVE BINDING PROTEIN 3) F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POM O.I. H.G. S.X.
0.38 46.7 0.71 At1g73390 843674 - F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;PFM O.I. H.G. S.X.
0.38 46.7 0.72 At4g34000 829547 ABF3 (ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR 3) Encodes an ABA-responsive element-binding protein with similarity to transcription factors that is expressed in response to stress and abscisic acid. O.I. H.G. S.X.
0.27 26.2 0.71 At1g72770 843609 HAB1 (HOMOLOGY TO ABI1) mutant has ABA hypersensitive inhibition of seed germination; Protein Phosphatase 2C O.I. H.G. S.X.
0.24 20.7 0.78 At4g26080 828714 ABI1 (ABA INSENSITIVE 1) Involved in abscisic acid (ABA) signal transduction. Negative regulator of ABA promotion of stomatal closure. O.I. H.G. S.X.
0.05 1.1 0.71 At1g22640 838870 MYB3 (MYB DOMAIN PROTEIN 3) MYB-type transcription factor (MYB3) that represses phenylpropanoid biosynthesis gene expression O.I. H.G. S.X.
0.03 0.6 0.75 At1g54100 841849 ALDH7B4 (Aldehyde Dehydrogenase 7B4) Aldehyde dehydrogenase 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	At3g29575	822619	AFP3 (ABI FIVE BINDING PROTEIN 3)	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;POM	O.I.	H.G.	S.X.
0.38	46.7	0.71	At1g73390	843674	-	F:molecular_function unknown;P:N-terminal protein myristoylation;C:cellular_component unknown;PFM	O.I.	H.G.	S.X.
0.38	46.7	0.72	At4g34000	829547	ABF3 (ABSCISIC ACID RESPONSIVE ELEMENTS-BINDING FACTOR 3)	Encodes an ABA-responsive element-binding protein with similarity to transcription factors that is expressed in response to stress and abscisic acid.	O.I.	H.G.	S.X.
0.27	26.2	0.71	At1g72770	843609	HAB1 (HOMOLOGY TO ABI1)	mutant has ABA hypersensitive inhibition of seed germination; Protein Phosphatase 2C	O.I.	H.G.	S.X.
0.24	20.7	0.78	At4g26080	828714	ABI1 (ABA INSENSITIVE 1)	Involved in abscisic acid (ABA) signal transduction. Negative regulator of ABA promotion of stomatal closure.	O.I.	H.G.	S.X.
0.05	1.1	0.71	At1g22640	838870	MYB3 (MYB DOMAIN PROTEIN 3)	MYB-type transcription factor (MYB3) that represses phenylpropanoid biosynthesis gene expression	O.I.	H.G.	S.X.
0.03	0.6	0.75	At1g54100	841849	ALDH7B4 (Aldehyde Dehydrogenase 7B4)	Aldehyde dehydrogenase	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
54.2 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
51.6 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
50.8 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
47.6 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.0 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.8 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.5 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.8 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.8 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.8 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
40.2 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.5 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.7 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.2 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.7 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.7 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.1 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.0 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.5 99.7 GSM184908 Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
31.1 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.2 99.6 GSM184907 Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
23.0 99.6 GSM133759 Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
22.2 99.6 GSM184909 Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
20.2 99.6 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
19.6 99.6 GSM133808 Diamond_A-1-Diamo-fum_SLD GSE5735 Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
15.7 99.5 GSM133811 Diamond_A-4-Diamo-fum_SLD GSE5735 Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
15.6 99.5 GSM266664 Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 3 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
15.1 99.4 GSM266665 Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 4 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
14.8 99.4 GSM13784 Cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
14.8 99.4 GSM133809 Diamond_A-2-Diamo-fum_SLD GSE5735 Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
14.7 99.4 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.6 99.4 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
14.2 99.4 GSM133810 Diamond_A-3-Diamo-fum_SLD GSE5735 Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
14.1 99.4 GSM184894 Arabidopsis, root cells, columella root cap, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
14.1 99.4 GSM184912 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
12.9 99.3 GSM133813 Diamond_A-2-Diamo-met_SLD GSE5735 Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
12.6 99.3 GSM270870 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
11.5 99.3 GSM184910 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
10.6 99.2 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.4 99.2 GSM184477 Lateral Root Cap root cells 2hr KCl control treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.3 99.2 GSM266666 Arabidopsis, root cells, columella root cap, -Fe, replicate 1 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
10.1 99.2 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
9.9 99.1 GSM184911 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
9.4 99.1 GSM133812 Diamond_A-1-Diamo-met_SLD GSE5735 Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
9.0 99.1 GSM128719 Pieterse_1-5_avrPstDC3000-12h_Rep1_ATH1 GSE5525 Transcriptome changes of Arabidopsis during pathogen and insect attack
8.8 99.0 GSM252688 Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep2 GSE9996 Organ regeneration in plants is independent of stem cell niche activity
8.7 99.0 GSM270868 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
8.6 99.0 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
8.6 99.0 GSM184893 Arabidopsis, root cells, columella root cap, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
54.2	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
51.6	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
50.8	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
47.6	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.0	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.8	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.5	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.8	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.8	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.8	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
40.2	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.5	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.7	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.2	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.7	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.7	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.1	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.0	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.5	99.7	GSM184908	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
31.1	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.2	99.6	GSM184907	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
23.0	99.6	GSM133759	Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
22.2	99.6	GSM184909	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
20.2	99.6	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
19.6	99.6	GSM133808	Diamond_A-1-Diamo-fum_SLD	GSE5735	Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
15.7	99.5	GSM133811	Diamond_A-4-Diamo-fum_SLD	GSE5735	Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
15.6	99.5	GSM266664	Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
15.1	99.4	GSM266665	Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 4	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
14.8	99.4	GSM13784	Cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
14.8	99.4	GSM133809	Diamond_A-2-Diamo-fum_SLD	GSE5735	Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
14.7	99.4	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.6	99.4	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
14.2	99.4	GSM133810	Diamond_A-3-Diamo-fum_SLD	GSE5735	Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
14.1	99.4	GSM184894	Arabidopsis, root cells, columella root cap, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
14.1	99.4	GSM184912	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
12.9	99.3	GSM133813	Diamond_A-2-Diamo-met_SLD	GSE5735	Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
12.6	99.3	GSM270870	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
11.5	99.3	GSM184910	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
10.6	99.2	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
10.4	99.2	GSM184477	Lateral Root Cap root cells 2hr KCl control treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.3	99.2	GSM266666	Arabidopsis, root cells, columella root cap, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
10.1	99.2	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
9.9	99.1	GSM184911	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
9.4	99.1	GSM133812	Diamond_A-1-Diamo-met_SLD	GSE5735	Identification of Core Genes Regulating Plant Programmed Cell Death (PCD)
9.0	99.1	GSM128719	Pieterse_1-5_avrPstDC3000-12h_Rep1_ATH1	GSE5525	Transcriptome changes of Arabidopsis during pathogen and insect attack
8.8	99.0	GSM252688	Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep2	GSE9996	Organ regeneration in plants is independent of stem cell niche activity
8.7	99.0	GSM270868	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
8.6	99.0	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
8.6	99.0	GSM184893	Arabidopsis, root cells, columella root cap, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.250 1 GO:0009800 The chemical reactions and pathways resulting in the formation of cinnamic acid, 3-phenyl-2-propenoic acid.
0.250 1 GO:0009892 Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
0.182 1 GO:0009787 Any process that modulates the frequency, rate or extent of signal transduction mediated by abscisic acid.

SF	Genes	GO ID	Process Name
0.250	1	GO:0009800	The chemical reactions and pathways resulting in the formation of cinnamic acid, 3-phenyl-2-propenoic acid.
0.250	1	GO:0009892	Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
0.182	1	GO:0009787	Any process that modulates the frequency, rate or extent of signal transduction mediated by abscisic acid.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.095 1 00340 Histidine metabolism
0.091 1 00310 Lysine degradation
0.087 1 00561 Glycerolipid metabolism

SF	Genes	KEGG ID	Pathway name
0.095	1	00340	Histidine metabolism
0.091	1	00310	Lysine degradation
0.087	1	00561	Glycerolipid metabolism

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	At3g29575
Gene name	AFP3 (ABI FIVE BINDING PROTEIN 3)
Module size	7 genes
NF	0.15
%ile	12.2

Co-expression analysis

Gene ID At3g29575 Gene name AFP3 (ABI FIVE BINDING PROTEIN 3) Module size 7 genes NF 0.15 %ile 12.2

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 KEGG0.095100340Histidine metabolism0.091100310Lysine degradation0.087100561Glycerolipid metabolism

Inter-species module comparison

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

Gene ID At3g29575

Gene name AFP3 (ABI FIVE BINDING PROTEIN 3)

Module size 7 genes

NF 0.15

%ile 12.2

: 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
0.095 1 00340 Histidine metabolism
0.091 1 00310 Lysine degradation
0.087 1 00561 Glycerolipid metabolism

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