CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At4g34970

Gene name ADF9 (ACTIN DEPOLYMERIZING FACTOR 9)

Module size 17 genes

NF 0.76

%ile 92.3

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
1.00 100.0 1.00 At4g34970 829649 ADF9 (ACTIN DEPOLYMERIZING FACTOR 9) F:actin binding;P:biological_process unknown;C:intracellular;MPOF O.I. H.G. S.X.
0.94 96.7 0.80 At1g26680 839209 transcriptional factor B3 family protein F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:chloroplast;POBM O.I. H.G. S.X.
0.90 95.1 0.77 At1g04180 837024 flavin-containing monooxygenase family protein / FMO family protein F:NADP or NADPH binding, oxidoreductase activity, monooxygenase activity, FAD binding, flavin-containing monooxygenase activity;P:unknown;C:unknown;BOFMPA O.I. H.G. S.X.
0.88 94.0 0.79 At1g04610 839474 flavin-containing monooxygenase / FMO (YUCCA3) F:oxidoreductase activity;P:auxin biosynthetic process;C:unknown;BOFMPA O.I. H.G. S.X.
0.85 92.4 0.78 At1g21340 838733 Dof-type zinc finger domain-containing protein F:transcription factor activity, DNA binding;P:regulation of transcription;C:cellular_component unknown;PO O.I. H.G. S.X.
0.80 89.8 0.79 At4g28720 828993 flavin-containing monooxygenase family protein / FMO family protein F:oxidoreductase activity, monooxygenase activity;P:unknown;C:unknown;BOFMPA O.I. H.G. S.X.
0.79 89.1 0.75 At3g01840 820047 protein kinase family protein F:protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, cell wall macromolecule catabolic process;C:endomembrane system;MPOFBVA O.I. H.G. S.X.
0.77 88.0 0.78 At5g57420 835848 IAA33 (INDOLE-3-ACETIC ACID INDUCIBLE 33) Belongs to auxin inducible gene family. O.I. H.G. S.X.
0.77 88.0 0.82 At2g04025 814929 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. H.G. S.X.
0.77 88.0 0.78 At4g18450 827576 ethylene-responsive factor, putative encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5. O.I. H.G. S.X.
0.73 85.5 0.74 At3g55550 824720 lectin protein kinase, putative F:kinase activity;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA O.I. H.G. S.X.
0.69 82.9 0.70 At2g46850 819298 ATP binding / protein kinase/ protein tyrosine kinase F:protein tyrosine kinase activity, protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:endomembrane system;PMOFBV O.I. H.G. S.X.
0.69 82.9 0.82 At2g21610 816699 pectinesterase family protein F:pectinesterase activity;P:N-terminal protein myristoylation, cell wall modification;C:cell wall, plant-type cell wall;PBFAMO O.I. H.G. S.X.
0.67 81.6 0.77 At5g51470 835221 auxin-responsive GH3 family protein F:molecular_function unknown;P:response to auxin stimulus;C:cellular_component unknown;POBMF O.I. H.G. S.X.
0.64 78.9 0.79 At4g26880 828795 stigma-specific Stig1 family protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BPOFM O.I. H.G. S.X.
0.61 76.7 0.79 At1g65570 842868 polygalacturonase, putative / pectinase, putative F:polygalacturonase activity;P:carbohydrate metabolic process;C:endomembrane system;FPBOMA O.I. H.G. S.X.
0.58 73.8 0.75 At1g07290 837240 nucleotide-sugar transmembrane transporter F:nucleotide-sugar transmembrane transporter activity;P:biological_process unknown;C:cellular_component unknown;MFPO O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
1.00	100.0	1.00	At4g34970	829649	ADF9 (ACTIN DEPOLYMERIZING FACTOR 9)	F:actin binding;P:biological_process unknown;C:intracellular;MPOF	O.I.	H.G.	S.X.
0.94	96.7	0.80	At1g26680	839209	transcriptional factor B3 family protein	F:transcription factor activity, DNA binding;P:regulation of transcription, DNA-dependent;C:chloroplast;POBM	O.I.	H.G.	S.X.
0.90	95.1	0.77	At1g04180	837024	flavin-containing monooxygenase family protein / FMO family protein	F:NADP or NADPH binding, oxidoreductase activity, monooxygenase activity, FAD binding, flavin-containing monooxygenase activity;P:unknown;C:unknown;BOFMPA	O.I.	H.G.	S.X.
0.88	94.0	0.79	At1g04610	839474	flavin-containing monooxygenase / FMO (YUCCA3)	F:oxidoreductase activity;P:auxin biosynthetic process;C:unknown;BOFMPA	O.I.	H.G.	S.X.
0.85	92.4	0.78	At1g21340	838733	Dof-type zinc finger domain-containing protein	F:transcription factor activity, DNA binding;P:regulation of transcription;C:cellular_component unknown;PO	O.I.	H.G.	S.X.
0.80	89.8	0.79	At4g28720	828993	flavin-containing monooxygenase family protein / FMO family protein	F:oxidoreductase activity, monooxygenase activity;P:unknown;C:unknown;BOFMPA	O.I.	H.G.	S.X.
0.79	89.1	0.75	At3g01840	820047	protein kinase family protein	F:protein tyrosine kinase activity, protein kinase activity, kinase activity, ATP binding;P:protein amino acid phosphorylation, cell wall macromolecule catabolic process;C:endomembrane system;MPOFBVA	O.I.	H.G.	S.X.
0.77	88.0	0.78	At5g57420	835848	IAA33 (INDOLE-3-ACETIC ACID INDUCIBLE 33)	Belongs to auxin inducible gene family.	O.I.	H.G.	S.X.
0.77	88.0	0.82	At2g04025	814929	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.77	88.0	0.78	At4g18450	827576	ethylene-responsive factor, putative	encodes a member of the ERF (ethylene response factor) subfamily B-3 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 18 members in this subfamily including ATERF-1, ATERF-2, AND ATERF-5.	O.I.	H.G.	S.X.
0.73	85.5	0.74	At3g55550	824720	lectin protein kinase, putative	F:kinase activity;P:protein amino acid phosphorylation;C:plasma membrane;MPOBFVA	O.I.	H.G.	S.X.
0.69	82.9	0.70	At2g46850	819298	ATP binding / protein kinase/ protein tyrosine kinase	F:protein tyrosine kinase activity, protein kinase activity, ATP binding;P:protein amino acid phosphorylation;C:endomembrane system;PMOFBV	O.I.	H.G.	S.X.
0.69	82.9	0.82	At2g21610	816699	pectinesterase family protein	F:pectinesterase activity;P:N-terminal protein myristoylation, cell wall modification;C:cell wall, plant-type cell wall;PBFAMO	O.I.	H.G.	S.X.
0.67	81.6	0.77	At5g51470	835221	auxin-responsive GH3 family protein	F:molecular_function unknown;P:response to auxin stimulus;C:cellular_component unknown;POBMF	O.I.	H.G.	S.X.
0.64	78.9	0.79	At4g26880	828795	stigma-specific Stig1 family protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BPOFM	O.I.	H.G.	S.X.
0.61	76.7	0.79	At1g65570	842868	polygalacturonase, putative / pectinase, putative	F:polygalacturonase activity;P:carbohydrate metabolic process;C:endomembrane system;FPBOMA	O.I.	H.G.	S.X.
0.58	73.8	0.75	At1g07290	837240	nucleotide-sugar transmembrane transporter	F:nucleotide-sugar transmembrane transporter activity;P:biological_process unknown;C:cellular_component unknown;MFPO	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
75.6 99.9 GSM284394 Arabidopsis GCE3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
54.6 99.8 GSM284392 Arabidopsis GCE1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
52.5 99.8 GSM311280 Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
45.8 99.8 GSM311279 Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
41.2 99.8 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
40.0 99.8 GSM284393 Arabidopsis GCE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
37.9 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
37.2 99.7 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.2 99.7 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
25.0 99.6 GSM133758 Lindsey_1-11_heart-stage-root_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
22.1 99.6 GSM133769 Lindsey_1-21_torpedo-basal_Rep6_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
19.8 99.6 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.3 99.5 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.3 99.5 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.6 99.5 GSM133772 Lindsey_1-24_torpedo-apical_Rep6_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.0 99.5 E-MEXP-1443-raw-cel-1581869573
16.6 99.5 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.1 99.5 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.8 99.5 GSM133771 Lindsey_1-23_torpedo-apical_Rep5_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.4 99.5 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.0 99.4 GSM133755 Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.6 99.4 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.4 99.4 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.0 99.4 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.9 99.4 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.5 99.4 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.3 99.4 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.3 99.3 GSM13783 Dexamethasone plus cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
10.8 99.2 GSM13784 Cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
10.3 99.2 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
10.3 99.2 GSM13780 Cycloheximide GSE911 Identification of LEAFY targets during reproductive transition
10.3 99.2 GSM13779 Dexamethasone plus cycloheximide GSE911 Identification of LEAFY targets during reproductive transition
10.2 99.2 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.1 99.2 GSM311292 Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
9.6 99.1 E-MEXP-1443-raw-cel-1581869515
8.9 99.0 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
75.6	99.9	GSM284394	Arabidopsis GCE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
54.6	99.8	GSM284392	Arabidopsis GCE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
52.5	99.8	GSM311280	Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
45.8	99.8	GSM311279	Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
41.2	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
40.0	99.8	GSM284393	Arabidopsis GCE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
37.9	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
37.2	99.7	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
32.2	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
25.0	99.6	GSM133758	Lindsey_1-11_heart-stage-root_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
22.1	99.6	GSM133769	Lindsey_1-21_torpedo-basal_Rep6_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
19.8	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.3	99.5	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.3	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.6	99.5	GSM133772	Lindsey_1-24_torpedo-apical_Rep6_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.0	99.5	E-MEXP-1443-raw-cel-1581869573
16.6	99.5	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.1	99.5	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.8	99.5	GSM133771	Lindsey_1-23_torpedo-apical_Rep5_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
15.4	99.5	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.0	99.4	GSM133755	Lindsey_1-7_heart-stage-cotyledon_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
14.6	99.4	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.4	99.4	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.0	99.4	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.9	99.4	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.5	99.4	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.3	99.4	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.3	99.3	GSM13783	Dexamethasone plus cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
10.8	99.2	GSM13784	Cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
10.3	99.2	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
10.3	99.2	GSM13780	Cycloheximide	GSE911	Identification of LEAFY targets during reproductive transition
10.3	99.2	GSM13779	Dexamethasone plus cycloheximide	GSE911	Identification of LEAFY targets during reproductive transition
10.2	99.2	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.1	99.2	GSM311292	Laser capture microdissected (LCM) chalazal endosperm at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
9.6	99.1	E-MEXP-1443-raw-cel-1581869515
8.9	99.0	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.105 1 GO:0015784 The directed movement of GDP-mannose into, out of, within or between cells. GDP-mannose is a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
0.071 1 GO:0009851 The chemical reactions and pathways resulting in the formation of auxins, plant hormones that regulate aspects of plant growth.
0.071 1 GO:0015780 The directed movement of nucleotide-sugars into, out of, within or between cells. Nucleotide-sugars are any nucleotide in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.

SF	Genes	GO ID	Process Name
0.105	1	GO:0015784	The directed movement of GDP-mannose into, out of, within or between cells. GDP-mannose is a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
0.071	1	GO:0009851	The chemical reactions and pathways resulting in the formation of auxins, plant hormones that regulate aspects of plant growth.
0.071	1	GO:0015780	The directed movement of nucleotide-sugars into, out of, within or between cells. Nucleotide-sugars are any nucleotide in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.037 1 00380 Tryptophan metabolism

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.037	1	00380	Tryptophan 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	At4g34970
Gene name	ADF9 (ACTIN DEPOLYMERIZING FACTOR 9)
Module size	17 genes
NF	0.76
%ile	92.3

Co-expression analysis

Gene ID At4g34970 Gene name ADF9 (ACTIN DEPOLYMERIZING FACTOR 9) Module size 17 genes NF 0.76 %ile 92.3

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 KEGG0.037100380Tryptophan 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 At4g34970

Gene name ADF9 (ACTIN DEPOLYMERIZING FACTOR 9)

Module size 17 genes

NF 0.76

%ile 92.3

: 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
0.037 1 00380 Tryptophan 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