CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g39760

Gene name BPM3

Module size 19 genes

NF 0.68

%ile 87.7

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
0.71 84.2 1.00 At2g39760 818561 BPM3 F:protein binding;P:biological_process unknown;C:unknown;MPOFV O.I. H.G. S.X.
0.86 93.1 0.93 At4g16100 827296 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. H.G. S.X.
0.84 91.9 0.92 At3g13340 820534 WD-40 repeat family protein F:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;BMFOPA O.I. H.G. S.X.
0.82 90.9 0.91 At1g04830 839404 RabGAP/TBC domain-containing protein F:RAB GTPase activator activity;P:regulation of Rab GTPase activity;C:intracellular;MOFPB O.I. H.G. S.X.
0.78 88.6 0.92 At1g56560 842110 beta-fructofuranosidase, putative / invertase, putative / saccharase, putative / beta-fructosidase, putative F:catalytic activity, beta-fructofuranosidase activity;P:biological_process unknown;C:unknown;OPB O.I. H.G. S.X.
0.75 86.9 0.93 At1g04790 839412 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFV O.I. H.G. S.X.
0.71 84.2 0.91 At2g01600 814689 epsin N-terminal homology (ENTH) domain-containing protein F:phospholipid binding, clathrin binding, binding, phosphatidylinositol binding;P:N-terminal protein myristoylation, clathrin coat assembly;C:membrane;MPFOB O.I. H.G. S.X.
0.67 81.6 0.92 At3g01200 821293 AtRP2 (PPDK regulatory protein 2) Encodes a PPDK regulatory protein that has protein kinase activity but lacks protein phosphatase activity towards PPDK (pyruvate orthophosphate dikinase). O.I. H.G. S.X.
0.67 81.6 0.91 At3g10030 820164 aspartate/glutamate/uridylate kinase family protein F:DNA binding;P:amino acid biosynthetic process;C:cytoplasm;BOPAMF O.I. H.G. S.X.
0.67 81.6 0.91 At3g21290 821683 dentin sialophosphoprotein-related F:molecular_function unknown;P:biological_process unknown;C:chloroplast;BMOFPVA O.I. H.G. S.X.
0.65 79.6 0.93 At3g24200 822006 FAD binding / monooxygenase/ oxidoreductase/ oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen F:oxidoreductase activity, monooxygenase activity, FAD binding, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;P:ubiquinone biosynthetic process, metabolic process;C:unknown;BOFMPA O.I. H.G. S.X.
0.65 79.6 0.92 At5g45360 834572 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOB O.I. H.G. S.X.
0.65 79.6 0.91 At4g33210 829457 F-box family protein (FBL15) F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:unknown;MPOFBV O.I. H.G. S.X.
0.65 79.6 0.93 At1g04230 839575 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBV O.I. H.G. S.X.
0.63 78.1 0.93 At5g53440 835425 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cytosol;MOFBPVA O.I. H.G. S.X.
0.62 77.3 0.92 At3g20800 821628 rcd1-like cell differentiation protein, putative F:molecular_function unknown;P:multicellular organismal development;C:cellular_component unknown;MFOP O.I. H.G. S.X.
0.60 75.7 0.94 At3g59380 825107 FTA (FARNESYLTRANSFERASE A) Encodes the alpha-subunit shared between protein farnesyltransferase and protein geranylgeranyltransferase-I. Involved in protein prenylation: covalent attachment of the C-15 isoprene farnesyl or the C-20 isoprene geranylgeranyl groups to the C-terminal end of some proteins. Involved in shoot and flower meristem homeostasis, and response to ABA and drought. Also regulates leaf cell shape. Mutant is epistatic to era1. O.I. H.G. S.X.
0.59 74.7 0.92 At1g71800 843510 cleavage stimulation factor, putative F:protein binding, RNA binding;P:biological_process unknown;C:cellular_component unknown;MPFOBA O.I. H.G. S.X.
0.58 73.8 0.91 At4g29790 829101 unknown protein F:molecular_function unknown;P:unknown;C:unknown;OMPFBV O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.71	84.2	1.00	At2g39760	818561	BPM3	F:protein binding;P:biological_process unknown;C:unknown;MPOFV	O.I.	H.G.	S.X.
0.86	93.1	0.93	At4g16100	827296	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	H.G.	S.X.
0.84	91.9	0.92	At3g13340	820534	WD-40 repeat family protein	F:molecular_function unknown;P:biological_process unknown;C:CUL4 RING ubiquitin ligase complex, heterotrimeric G-protein complex;BMFOPA	O.I.	H.G.	S.X.
0.82	90.9	0.91	At1g04830	839404	RabGAP/TBC domain-containing protein	F:RAB GTPase activator activity;P:regulation of Rab GTPase activity;C:intracellular;MOFPB	O.I.	H.G.	S.X.
0.78	88.6	0.92	At1g56560	842110	beta-fructofuranosidase, putative / invertase, putative / saccharase, putative / beta-fructosidase, putative	F:catalytic activity, beta-fructofuranosidase activity;P:biological_process unknown;C:unknown;OPB	O.I.	H.G.	S.X.
0.75	86.9	0.93	At1g04790	839412	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:unknown;PMOFV	O.I.	H.G.	S.X.
0.71	84.2	0.91	At2g01600	814689	epsin N-terminal homology (ENTH) domain-containing protein	F:phospholipid binding, clathrin binding, binding, phosphatidylinositol binding;P:N-terminal protein myristoylation, clathrin coat assembly;C:membrane;MPFOB	O.I.	H.G.	S.X.
0.67	81.6	0.92	At3g01200	821293	AtRP2 (PPDK regulatory protein 2)	Encodes a PPDK regulatory protein that has protein kinase activity but lacks protein phosphatase activity towards PPDK (pyruvate orthophosphate dikinase).	O.I.	H.G.	S.X.
0.67	81.6	0.91	At3g10030	820164	aspartate/glutamate/uridylate kinase family protein	F:DNA binding;P:amino acid biosynthetic process;C:cytoplasm;BOPAMF	O.I.	H.G.	S.X.
0.67	81.6	0.91	At3g21290	821683	dentin sialophosphoprotein-related	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;BMOFPVA	O.I.	H.G.	S.X.
0.65	79.6	0.93	At3g24200	822006	FAD binding / monooxygenase/ oxidoreductase/ oxidoreductase, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen	F:oxidoreductase activity, monooxygenase activity, FAD binding, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;P:ubiquinone biosynthetic process, metabolic process;C:unknown;BOFMPA	O.I.	H.G.	S.X.
0.65	79.6	0.92	At5g45360	834572	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOB	O.I.	H.G.	S.X.
0.65	79.6	0.91	At4g33210	829457	F-box family protein (FBL15)	F:ubiquitin-protein ligase activity;P:ubiquitin-dependent protein catabolic process;C:unknown;MPOFBV	O.I.	H.G.	S.X.
0.65	79.6	0.93	At1g04230	839575	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPBV	O.I.	H.G.	S.X.
0.63	78.1	0.93	At5g53440	835425	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cytosol;MOFBPVA	O.I.	H.G.	S.X.
0.62	77.3	0.92	At3g20800	821628	rcd1-like cell differentiation protein, putative	F:molecular_function unknown;P:multicellular organismal development;C:cellular_component unknown;MFOP	O.I.	H.G.	S.X.
0.60	75.7	0.94	At3g59380	825107	FTA (FARNESYLTRANSFERASE A)	Encodes the alpha-subunit shared between protein farnesyltransferase and protein geranylgeranyltransferase-I. Involved in protein prenylation: covalent attachment of the C-15 isoprene farnesyl or the C-20 isoprene geranylgeranyl groups to the C-terminal end of some proteins. Involved in shoot and flower meristem homeostasis, and response to ABA and drought. Also regulates leaf cell shape. Mutant is epistatic to era1.	O.I.	H.G.	S.X.
0.59	74.7	0.92	At1g71800	843510	cleavage stimulation factor, putative	F:protein binding, RNA binding;P:biological_process unknown;C:cellular_component unknown;MPFOBA	O.I.	H.G.	S.X.
0.58	73.8	0.91	At4g29790	829101	unknown protein	F:molecular_function unknown;P:unknown;C:unknown;OMPFBV	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
69.2 99.9 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
22.8 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
21.6 99.6 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.3 99.6 GSM131609 ATGE_43_A GSE5632 AtGenExpress: Developmental series (flowers and pollen)
18.3 99.5 GSM131610 ATGE_43_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
17.7 99.5 GSM131606 ATGE_42_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
16.7 99.5 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2 99.5 GSM131607 ATGE_42_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
16.1 99.5 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.1 99.5 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
15.9 99.5 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.3 99.4 GSM131611 ATGE_43_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
14.8 99.4 GSM184893 Arabidopsis, root cells, columella root cap, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
14.6 99.4 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5 99.4 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.4 99.4 GSM184894 Arabidopsis, root cells, columella root cap, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
14.3 99.4 GSM266668 Arabidopsis, root cells, columella root cap, -Fe, replicate 3 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
14.2 99.4 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.0 99.4 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.9 99.4 GSM131608 ATGE_42_D GSE5632 AtGenExpress: Developmental series (flowers and pollen)
13.6 99.4 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.5 99.4 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.2 99.4 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.8 99.3 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.6 99.3 GSM266667 Arabidopsis, root cells, columella root cap, -Fe, replicate 2 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
12.5 99.3 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.4 99.3 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.9 99.3 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.8 99.3 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.8 99.3 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.0 99.2 GSM184892 Arabidopsis, root cells, columella root cap, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
10.3 99.2 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.6 99.1 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.0 99.1 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
69.2	99.9	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
22.8	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
21.6	99.6	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.3	99.6	GSM131609	ATGE_43_A	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
18.3	99.5	GSM131610	ATGE_43_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
17.7	99.5	GSM131606	ATGE_42_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
16.7	99.5	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2	99.5	GSM131607	ATGE_42_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
16.1	99.5	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.1	99.5	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
15.9	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.3	99.4	GSM131611	ATGE_43_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
14.8	99.4	GSM184893	Arabidopsis, root cells, columella root cap, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
14.6	99.4	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5	99.4	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.4	99.4	GSM184894	Arabidopsis, root cells, columella root cap, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
14.3	99.4	GSM266668	Arabidopsis, root cells, columella root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
14.2	99.4	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.0	99.4	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.9	99.4	GSM131608	ATGE_42_D	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
13.6	99.4	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.5	99.4	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.2	99.4	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.8	99.3	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.6	99.3	GSM266667	Arabidopsis, root cells, columella root cap, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
12.5	99.3	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.4	99.3	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.9	99.3	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.8	99.3	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.8	99.3	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.0	99.2	GSM184892	Arabidopsis, root cells, columella root cap, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
10.3	99.2	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.6	99.1	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.0	99.1	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.100 1 GO:0018347 The covalent attachment of a farnesyl moiety to a protein amino acid.
0.095 1 GO:0008360 Any process that modulates the surface configuration of a cell.
0.095 1 GO:0018348 The covalent attachment of a geranylgeranyl moiety to a protein amino acid.

SF	Genes	GO ID	Process Name
0.100	1	GO:0018347	The covalent attachment of a farnesyl moiety to a protein amino acid.
0.095	1	GO:0008360	Any process that modulates the surface configuration of a cell.
0.095	1	GO:0018348	The covalent attachment of a geranylgeranyl moiety to a protein amino acid.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.045 1 00130 Ubiquinone and other terpenoid-quinone biosynthesis
0.030 1 03018 RNA degradation
0.002 1 01100 Metabolic pathways

SF	Genes	KEGG ID	Pathway name
0.045	1	00130	Ubiquinone and other terpenoid-quinone biosynthesis
0.030	1	03018	RNA degradation
0.002	1	01100	Metabolic pathways

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

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Gene ID	At2g39760
Gene name	BPM3
Module size	19 genes
NF	0.68
%ile	87.7

Co-expression analysis

Gene ID At2g39760 Gene name BPM3 Module size 19 genes NF 0.68 %ile 87.7

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 AmiGO0.1001GO:0018347The covalent attachment of a farnesyl moiety to a protein amino acid.0.0951GO:0008360Any process that modulates the surface configuration of a cell.0.0951GO:0018348The covalent attachment of a geranylgeranyl moiety to a protein amino acid.

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.045100130Ubiquinone and other terpenoid-quinone biosynthesis0.030103018RNA degradation0.002101100Metabolic pathways

Inter-species module comparison

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

Gene ID At2g39760

Gene name BPM3

Module size 19 genes

NF 0.68

%ile 87.7

: 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
0.045 1 00130 Ubiquinone and other terpenoid-quinone biosynthesis
0.030 1 03018 RNA degradation
0.002 1 01100 Metabolic pathways

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