CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g25500

Gene name choline transporter-related

Module size 9 genes

NF 0.47

%ile 66.0

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
1.00 100.0 1.00 At1g25500 839136 choline transporter-related F:unknown;P:biological_process unknown;C:chloroplast;MFOP O.I. H.G. S.X.
0.55 70.6 0.83 At1g05120 839319 SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing protein F:in 6 functions;P:unknown;C:unknown;MFBOPVA O.I. H.G. S.X.
0.53 68.6 0.83 At5g49220 834982 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. H.G. S.X.
0.48 62.5 0.84 At5g49610 835023 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO O.I. H.G. S.X.
0.43 55.3 0.83 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.
0.38 46.7 0.83 At5g16800 831543 GCN5-related N-acetyltransferase (GNAT) family protein F:N-acetyltransferase activity;P:metabolic process;C:cellular_component unknown;MOBPAFV O.I. H.G. S.X.
0.36 43.6 0.84 At2g39760 818561 BPM3 F:protein binding;P:biological_process unknown;C:unknown;MPOFV O.I. H.G. S.X.
0.36 43.6 0.83 At3g24740 822072 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.33 38.1 0.84 At5g58510 835964 unknown protein F:molecular_function unknown;P:biological_process unknown;C:chloroplast;MPOB 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	At1g25500	839136	choline transporter-related	F:unknown;P:biological_process unknown;C:chloroplast;MFOP	O.I.	H.G.	S.X.
0.55	70.6	0.83	At1g05120	839319	SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing protein	F:in 6 functions;P:unknown;C:unknown;MFBOPVA	O.I.	H.G.	S.X.
0.53	68.6	0.83	At5g49220	834982	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	H.G.	S.X.
0.48	62.5	0.84	At5g49610	835023	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PMO	O.I.	H.G.	S.X.
0.43	55.3	0.83	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.
0.38	46.7	0.83	At5g16800	831543	GCN5-related N-acetyltransferase (GNAT) family protein	F:N-acetyltransferase activity;P:metabolic process;C:cellular_component unknown;MOBPAFV	O.I.	H.G.	S.X.
0.36	43.6	0.84	At2g39760	818561	BPM3	F:protein binding;P:biological_process unknown;C:unknown;MPOFV	O.I.	H.G.	S.X.
0.36	43.6	0.83	At3g24740	822072	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.33	38.1	0.84	At5g58510	835964	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;MPOB	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
182.2 100.0 GSM133759 Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
36.7 99.7 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
30.1 99.7 GSM184893 Arabidopsis, root cells, columella root cap, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
29.6 99.7 GSM266668 Arabidopsis, root cells, columella root cap, -Fe, replicate 3 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
29.4 99.7 GSM184894 Arabidopsis, root cells, columella root cap, standard conditions, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
25.3 99.6 GSM266667 Arabidopsis, root cells, columella root cap, -Fe, replicate 2 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
21.8 99.6 GSM184892 Arabidopsis, root cells, columella root cap, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
16.1 99.5 GSM266666 Arabidopsis, root cells, columella root cap, -Fe, replicate 1 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
15.5 99.5 GSM184516 Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
15.0 99.4 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.6 99.4 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.0 99.4 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.7 99.4 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.1 99.4 GSM184518 Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
13.1 99.4 GSM184895 Arabidopsis, root cells, cortex, standard conditions, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
12.5 99.3 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.3 99.3 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
12.3 99.3 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.3 99.3 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.1 99.3 GSM284389 Arabidopsis GMPE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.1 99.3 GSM184487 Epidermis&Cortex root cells 2hr KCl control treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
12.0 99.3 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.0 99.3 GSM184486 Epidermis&Cortex root cells 2hr KCl control treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
11.6 99.3 GSM284387 Arabidopsis GSUS4b GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.5 99.3 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
11.4 99.3 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.1 99.2 GSM184519 Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
11.0 99.2 E-ATMX-1-raw-cel-1112746095
10.8 99.2 GSM184896 Arabidopsis, root cells, cortex, standard conditions, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
10.8 99.2 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.6 99.2 GSM284384 Arabidopsis GEP5 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.2 99.2 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
9.8 99.1 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
9.8 99.1 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7 99.1 GSM184504 Pericycle root cells 2hr KCl control treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.6 99.1 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.4 99.1 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.2 99.1 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.2 99.1 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.1 99.1 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.0 99.1 GSM265473 Arabidopsis, whole roots, -Fe, 72 hour, rep 1 GSE10502 Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
8.9 99.0 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8 99.0 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
182.2	100.0	GSM133759	Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
36.7	99.7	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
30.1	99.7	GSM184893	Arabidopsis, root cells, columella root cap, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
29.6	99.7	GSM266668	Arabidopsis, root cells, columella root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
29.4	99.7	GSM184894	Arabidopsis, root cells, columella root cap, standard conditions, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
25.3	99.6	GSM266667	Arabidopsis, root cells, columella root cap, -Fe, replicate 2	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
21.8	99.6	GSM184892	Arabidopsis, root cells, columella root cap, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
16.1	99.5	GSM266666	Arabidopsis, root cells, columella root cap, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
15.5	99.5	GSM184516	Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
15.0	99.4	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.6	99.4	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.0	99.4	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.7	99.4	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.1	99.4	GSM184518	Pericycle root cells 2hr continuous KCl and MSX control treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
13.1	99.4	GSM184895	Arabidopsis, root cells, cortex, standard conditions, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
12.5	99.3	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.3	99.3	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
12.3	99.3	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.3	99.3	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.1	99.3	GSM284389	Arabidopsis GMPE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
12.1	99.3	GSM184487	Epidermis&Cortex root cells 2hr KCl control treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
12.0	99.3	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.0	99.3	GSM184486	Epidermis&Cortex root cells 2hr KCl control treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.6	99.3	GSM284387	Arabidopsis GSUS4b	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.5	99.3	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
11.4	99.3	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.1	99.2	GSM184519	Pericycle root cells 2hr continuous KNO3 and MSX treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.0	99.2	E-ATMX-1-raw-cel-1112746095
10.8	99.2	GSM184896	Arabidopsis, root cells, cortex, standard conditions, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
10.8	99.2	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.6	99.2	GSM284384	Arabidopsis GEP5	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
10.2	99.2	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
9.8	99.1	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
9.8	99.1	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7	99.1	GSM184504	Pericycle root cells 2hr KCl control treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.6	99.1	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.4	99.1	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.2	99.1	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.2	99.1	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.1	99.1	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.0	99.1	GSM265473	Arabidopsis, whole roots, -Fe, 72 hour, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
8.9	99.0	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8	99.0	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1

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	At1g25500
Gene name	choline transporter-related
Module size	9 genes
NF	0.47
%ile	66.0

Co-expression analysis

Gene ID At1g25500 Gene name choline transporter-related Module size 9 genes NF 0.47 %ile 66.0

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 At1g25500

Gene name choline transporter-related

Module size 9 genes

NF 0.47

%ile 66.0

: 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