CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g60910

Gene name AGL8 (agamous-like 8)

Module size 5 genes

NF 0.47

%ile 66.6

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
0.40 50.8 1.00 At5g60910 836212 AGL8 (agamous-like 8) MADS box gene negatively regulated by APETALA1 O.I. H.G. S.X.
0.53 68.6 0.72 At5g67110 836846 ALC (ALCATRAZ) encodes a myc/bHLH transcription factor-like protein. Gene product is involved in fruit dehiscence. Mutant siliques fail to dehisce. O.I. H.G. S.X.
0.50 65.3 0.70 At4g35190 829672 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOPFAM O.I. H.G. S.X.
0.50 65.3 0.72 At5g44630 834491 terpene synthase/cyclase family protein Encodes a sesquiterpene synthase involved in generating all of the group B sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in intrafloral nectaries. O.I. H.G. S.X.
0.46 59.8 0.69 At4g31610 829288 REM1 (REPRODUCTIVE MERISTEM 1) Expressed specifically in reproductive meristems, member of a moderately sized gene family distantly related to known plant DNA binding proteins O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.40	50.8	1.00	At5g60910	836212	AGL8 (agamous-like 8)	MADS box gene negatively regulated by APETALA1	O.I.	H.G.	S.X.
0.53	68.6	0.72	At5g67110	836846	ALC (ALCATRAZ)	encodes a myc/bHLH transcription factor-like protein. Gene product is involved in fruit dehiscence. Mutant siliques fail to dehisce.	O.I.	H.G.	S.X.
0.50	65.3	0.70	At4g35190	829672	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;BOPFAM	O.I.	H.G.	S.X.
0.50	65.3	0.72	At5g44630	834491	terpene synthase/cyclase family protein	Encodes a sesquiterpene synthase involved in generating all of the group B sesquiterpenes found in the Arabidopsis floral volatile blend. Strongly expressed in intrafloral nectaries.	O.I.	H.G.	S.X.
0.46	59.8	0.69	At4g31610	829288	REM1 (REPRODUCTIVE MERISTEM 1)	Expressed specifically in reproductive meristems, member of a moderately sized gene family distantly related to known plant DNA binding proteins	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
134.4 99.9 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
99.4 99.9 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
92.8 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
89.0 99.9 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
52.8 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.1 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.1 99.8 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
49.8 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.1 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.4 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
42.6 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.4 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.8 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.3 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.8 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.2 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
34.7 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.5 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.1 99.7 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
31.5 99.7 GSM311291 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
29.2 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
27.9 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.5 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.4 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
25.8 99.7 E-MEXP-1443-raw-cel-1581869745
23.9 99.6 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.1 99.6 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
22.1 99.6 GSM184911 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
21.6 99.6 E-MEXP-1443-raw-cel-1581869803
19.3 99.6 GSM184910 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
18.6 99.5 GSM131322 AtGen_6-3422_Saltstress-Roots-6.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
16.4 99.5 GSM284392 Arabidopsis GCE1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
15.7 99.5 E-MEXP-807-raw-cel-1173272948
15.6 99.5 GSM131318 AtGen_6-3322_Saltstress-Roots-3.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
14.7 99.4 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.5 99.4 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
14.1 99.4 GSM284394 Arabidopsis GCE3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
13.8 99.4 GSM131321 AtGen_6-3421_Saltstress-Roots-6.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
13.2 99.4 GSM266668 Arabidopsis, root cells, columella root cap, -Fe, replicate 3 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
12.3 99.3 GSM284393 Arabidopsis GCE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.7 99.3 GSM131317 AtGen_6-3321_Saltstress-Roots-3.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
11.6 99.3 GSM184912 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
10.9 99.2 GSM133968 Birnbaum_1-19_LRC-1_Rep1_ATH1 GSE5749 A gene expression map of the Arabidopsis root
10.9 99.2 GSM184923 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
10.7 99.2 E-MEXP-807-raw-cel-1173273170
10.6 99.2 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
9.6 99.1 GSM184635 Arabidopsis, root cells, 140 mM NaCl, replicate 2 GSE7636 Expression analysis of the effect of protoplasting and FACS sorting in roots
9.5 99.1 GSM133969 Birnbaum_1-20_LRC-2_Rep2_ATH1 GSE5749 A gene expression map of the Arabidopsis root
9.2 99.1 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
9.2 99.1 GSM184917 Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
8.7 99.0 GSM266667 Arabidopsis, root cells, columella root cap, -Fe, replicate 2 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
8.6 99.0 GSM184899 Arabidopsis, root cells, endodermis and quiescent center, 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
134.4	99.9	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
99.4	99.9	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
92.8	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
89.0	99.9	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
52.8	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.1	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.1	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
49.8	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.1	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.4	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
42.6	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.4	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.8	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.3	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.8	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.2	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
34.7	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.5	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.1	99.7	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
31.5	99.7	GSM311291	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
29.2	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.9	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.5	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.4	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
25.8	99.7	E-MEXP-1443-raw-cel-1581869745
23.9	99.6	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
23.1	99.6	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.1	99.6	GSM184911	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
21.6	99.6	E-MEXP-1443-raw-cel-1581869803
19.3	99.6	GSM184910	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
18.6	99.5	GSM131322	AtGen_6-3422_Saltstress-Roots-6.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
16.4	99.5	GSM284392	Arabidopsis GCE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
15.7	99.5	E-MEXP-807-raw-cel-1173272948
15.6	99.5	GSM131318	AtGen_6-3322_Saltstress-Roots-3.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
14.7	99.4	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.5	99.4	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
14.1	99.4	GSM284394	Arabidopsis GCE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
13.8	99.4	GSM131321	AtGen_6-3421_Saltstress-Roots-6.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
13.2	99.4	GSM266668	Arabidopsis, root cells, columella root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
12.3	99.3	GSM284393	Arabidopsis GCE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.7	99.3	GSM131317	AtGen_6-3321_Saltstress-Roots-3.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
11.6	99.3	GSM184912	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
10.9	99.2	GSM133968	Birnbaum_1-19_LRC-1_Rep1_ATH1	GSE5749	A gene expression map of the Arabidopsis root
10.9	99.2	GSM184923	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
10.7	99.2	E-MEXP-807-raw-cel-1173273170
10.6	99.2	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
9.6	99.1	GSM184635	Arabidopsis, root cells, 140 mM NaCl, replicate 2	GSE7636	Expression analysis of the effect of protoplasting and FACS sorting in roots
9.5	99.1	GSM133969	Birnbaum_1-20_LRC-2_Rep2_ATH1	GSE5749	A gene expression map of the Arabidopsis root
9.2	99.1	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
9.2	99.1	GSM184917	Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
8.7	99.0	GSM266667	Arabidopsis, root cells, columella root cap, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
8.6	99.0	GSM184899	Arabidopsis, root cells, endodermis and quiescent center, 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
0.286 1 GO:0051762 The chemical reactions and pathways resulting in the formation of sesquiterpenes, any of a class of terpenes of the formula C15H24 or a derivative of such a terpene.
0.222 1 GO:0016106 The chemical reactions and pathways resulting in the formation of sesquiterpenoid compounds, terpenoids with three isoprene units.
0.154 1 GO:0010047 The process leading to the spontaneous opening of the fruit permitting the escape of seeds.

SF	Genes	GO ID	Process Name
0.286	1	GO:0051762	The chemical reactions and pathways resulting in the formation of sesquiterpenes, any of a class of terpenes of the formula C15H24 or a derivative of such a terpene.
0.222	1	GO:0016106	The chemical reactions and pathways resulting in the formation of sesquiterpenoid compounds, terpenoids with three isoprene units.
0.154	1	GO:0010047	The process leading to the spontaneous opening of the fruit permitting the escape of seeds.

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	At5g60910
Gene name	AGL8 (agamous-like 8)
Module size	5 genes
NF	0.47
%ile	66.6

Co-expression analysis

Gene ID At5g60910 Gene name AGL8 (agamous-like 8) Module size 5 genes NF 0.47 %ile 66.6

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 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 At5g60910

Gene name AGL8 (agamous-like 8)

Module size 5 genes

NF 0.47

%ile 66.6

: 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

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