CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g28540

Gene name nucleic acid binding / nucleotide binding / protein binding / zinc ion binding

Module size 8 genes

NF 0.36

%ile 48.5

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
0.29 30.3 1.00 At2g28540 817402 nucleic acid binding / nucleotide binding / protein binding / zinc ion binding F:protein binding, nucleotide binding, zinc ion binding, nucleic acid binding;P:unknown;C:unknown;OMFPB O.I. H.G. S.X.
0.61 76.7 0.92 At3g59000 825069 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.42 53.9 0.92 At3g51640 824327 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;MOFBPVA O.I. H.G. S.X.
0.40 50.8 0.93 At1g05910 837101 cell division cycle protein 48-related / CDC48-related F:nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:unknown;C:unknown;BMOFPAV O.I. H.G. S.X.
0.40 50.8 0.92 At4g29790 829101 unknown protein F:molecular_function unknown;P:unknown;C:unknown;OMPFBV O.I. H.G. S.X.
0.36 43.6 0.92 At3g12640 820444 RNA binding / nucleic acid binding / nucleotide binding F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFBOV O.I. H.G. S.X.
0.32 35.7 0.92 At3g21290 821683 dentin sialophosphoprotein-related F:molecular_function unknown;P:biological_process unknown;C:chloroplast;BMOFPVA O.I. H.G. S.X.
0.21 15.8 0.93 At2g32760 817836 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOB O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.29	30.3	1.00	At2g28540	817402	nucleic acid binding / nucleotide binding / protein binding / zinc ion binding	F:protein binding, nucleotide binding, zinc ion binding, nucleic acid binding;P:unknown;C:unknown;OMFPB	O.I.	H.G.	S.X.
0.61	76.7	0.92	At3g59000	825069	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.42	53.9	0.92	At3g51640	824327	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;MOFBPVA	O.I.	H.G.	S.X.
0.40	50.8	0.93	At1g05910	837101	cell division cycle protein 48-related / CDC48-related	F:nucleoside-triphosphatase activity, nucleotide binding, ATP binding;P:unknown;C:unknown;BMOFPAV	O.I.	H.G.	S.X.
0.40	50.8	0.92	At4g29790	829101	unknown protein	F:molecular_function unknown;P:unknown;C:unknown;OMPFBV	O.I.	H.G.	S.X.
0.36	43.6	0.92	At3g12640	820444	RNA binding / nucleic acid binding / nucleotide binding	F:RNA binding, nucleotide binding, nucleic acid binding;P:biological_process unknown;C:cellular_component unknown;MPFBOV	O.I.	H.G.	S.X.
0.32	35.7	0.92	At3g21290	821683	dentin sialophosphoprotein-related	F:molecular_function unknown;P:biological_process unknown;C:chloroplast;BMOFPVA	O.I.	H.G.	S.X.
0.21	15.8	0.93	At2g32760	817836	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFPOB	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
28.5 99.7 GSM142904 WW002_ATH1_A1-willa-CON-REP2 GSE6181 Assembly of the cell wall pectic matrix.
27.5 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.3 99.6 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.9 99.6 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
19.4 99.6 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.3 99.6 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.3 99.5 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.9 99.5 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.7 99.5 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.1 99.4 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.0 99.4 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.0 99.4 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.8 99.4 GSM184487 Epidermis&Cortex root cells 2hr KCl control treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
14.3 99.4 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.3 99.4 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.2 99.4 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.2 99.4 GSM142902 WW001_ATH1_A1-WILLA-CON GSE6181 Assembly of the cell wall pectic matrix.
14.0 99.4 GSM184477 Lateral Root Cap root cells 2hr KCl control treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
13.6 99.4 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.3 99.4 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.1 99.4 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.3 99.3 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.1 99.3 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
12.0 99.3 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.3 99.3 E-ATMX-31-raw-cel-1516947916
10.4 99.2 E-ATMX-31-raw-cel-1516947899
10.4 99.2 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.2 99.2 GSM184484 Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.0 99.2 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.6 99.1 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
9.5 99.1 GSM133962 Fukuda_1-7_6A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.4 99.1 E-ATMX-13-raw-cel-1556149743
9.2 99.1 GSM184482 Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
8.9 99.0 GSM133963 Fukuda_1-8_6B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
28.5	99.7	GSM142904	WW002_ATH1_A1-willa-CON-REP2	GSE6181	Assembly of the cell wall pectic matrix.
27.5	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.3	99.6	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.9	99.6	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.4	99.6	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.3	99.6	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.3	99.5	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.9	99.5	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.7	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.1	99.4	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.0	99.4	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.0	99.4	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.8	99.4	GSM184487	Epidermis&Cortex root cells 2hr KCl control treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
14.3	99.4	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.3	99.4	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.2	99.4	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.2	99.4	GSM142902	WW001_ATH1_A1-WILLA-CON	GSE6181	Assembly of the cell wall pectic matrix.
14.0	99.4	GSM184477	Lateral Root Cap root cells 2hr KCl control treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
13.6	99.4	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.3	99.4	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.1	99.4	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.3	99.3	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.1	99.3	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
12.0	99.3	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.3	99.3	E-ATMX-31-raw-cel-1516947916
10.4	99.2	E-ATMX-31-raw-cel-1516947899
10.4	99.2	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.2	99.2	GSM184484	Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.0	99.2	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.6	99.1	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
9.5	99.1	GSM133962	Fukuda_1-7_6A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.4	99.1	E-ATMX-13-raw-cel-1556149743
9.2	99.1	GSM184482	Lateral Root Cap root cells 2hr continuous KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
8.9	99.0	GSM133963	Fukuda_1-8_6B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.

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	At2g28540
Gene name	nucleic acid binding / nucleotide binding / protein binding / zinc ion binding
Module size	8 genes
NF	0.36
%ile	48.5

Co-expression analysis

Gene ID At2g28540 Gene name nucleic acid binding / nucleotide binding / protein binding / zinc ion binding Module size 8 genes NF 0.36 %ile 48.5

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 At2g28540

Gene name nucleic acid binding / nucleotide binding / protein binding / zinc ion binding

Module size 8 genes

NF 0.36

%ile 48.5

: 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