CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g16600

Gene name SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing protein

Module size 5 genes

NF 0.18

%ile 15.4

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
0.10 3.4 1.00 At3g16600 820911 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.
0.33 38.1 0.82 At4g16930 827401 disease resistance protein (TIR-NBS-LRR class), putative F:transmembrane receptor activity;P:signal transduction, defense response, innate immune response;C:intrinsic to membrane;P O.I. H.G. S.X.
0.29 30.3 0.81 At1g23610 838971 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.27 26.2 0.82 At2g37610 818338 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.24 20.7 0.83 At4g02910 828141 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.10	3.4	1.00	At3g16600	820911	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.
0.33	38.1	0.82	At4g16930	827401	disease resistance protein (TIR-NBS-LRR class), putative	F:transmembrane receptor activity;P:signal transduction, defense response, innate immune response;C:intrinsic to membrane;P	O.I.	H.G.	S.X.
0.29	30.3	0.81	At1g23610	838971	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.27	26.2	0.82	At2g37610	818338	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.24	20.7	0.83	At4g02910	828141	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	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
73.9 99.9 GSM183515 ATR1_OE_rep1 GSE7570 ATR1_like_Clade_OE_and_miR
49.3 99.8 GSM270868 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
48.7 99.8 GSM270870 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
34.4 99.7 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
33.9 99.7 GSM265474 Arabidopsis, whole roots, -Fe, 72 hour, rep 2 GSE10502 Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
30.6 99.7 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.6 99.7 GSM265473 Arabidopsis, whole roots, -Fe, 72 hour, rep 1 GSE10502 Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
26.0 99.7 GSM133293 NO.30 GSE5698 AtGenExpress: Cytokinin treatment of seedlings
25.4 99.6 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
23.7 99.6 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
23.5 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
23.1 99.6 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.3 99.6 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
22.0 99.6 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.8 99.6 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.5 99.6 E-ATMX-13-raw-cel-1556149919
20.9 99.6 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.6 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
20.2 99.6 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.9 99.6 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
19.5 99.6 GSM265471 Arabidopsis, whole roots, -Fe, 48 hour, rep 1 GSE10502 Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
19.0 99.5 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.2 99.5 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.1 99.5 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.0 99.5 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.0 99.5 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.9 99.5 GSM142902 WW001_ATH1_A1-WILLA-CON GSE6181 Assembly of the cell wall pectic matrix.
17.8 99.5 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.1 99.5 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.8 99.5 GSM125254 Seedling_OEA3L5_rep1 GSE5465 Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
16.3 99.5 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.1 99.4 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.6 99.4 GSM131160 AtGen_C-10_1-Pi-6_REP1_ATH1 GSE5616 AtGenExpress: Response to Phytophthora infestans
14.6 99.4 GSM131161 AtGen_C-11_2-Pi-6_REP2_ATH1 GSE5616 AtGenExpress: Response to Phytophthora infestans
13.9 99.4 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.8 99.4 E-ATMX-13-raw-cel-1556149807
13.4 99.4 GSM184151 ATR1_OE_rep2 GSE7570 ATR1_like_Clade_OE_and_miR
13.3 99.4 GSM125255 Seedling_OEA3L5_rep2 GSE5465 Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
12.9 99.3 GSM131162 AtGen_C-12_3-Pi-6_REP3_ATH1 GSE5616 AtGenExpress: Response to Phytophthora infestans
12.8 99.3 GSM125256 Seedling_OETOP6B_rep1 GSE5465 Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
12.8 99.3 GSM265472 Arabidopsis, whole roots, -Fe, 48 hour, rep 2 GSE10502 Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
11.2 99.2 E-ATMX-13-raw-cel-1556149871
11.1 99.2 GSM142904 WW002_ATH1_A1-willa-CON-REP2 GSE6181 Assembly of the cell wall pectic matrix.
11.0 99.2 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.0 99.2 E-ATMX-13-raw-cel-1556149759
9.9 99.1 GSM131164 AtGen_C-14_2-Pi-12_REP2_ATH1 GSE5616 AtGenExpress: Response to Phytophthora infestans
8.8 99.0 GSM125257 Seedling_OETOP6B_rep2 GSE5465 Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
8.8 99.0 E-NASC-76-raw-cel-1359879158
8.7 99.0 GSM183513 MYB29_OE_rep1 GSE7570 ATR1_like_Clade_OE_and_miR
8.6 99.0 E-MEXP-807-raw-cel-1173272921

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
73.9	99.9	GSM183515	ATR1_OE_rep1	GSE7570	ATR1_like_Clade_OE_and_miR
49.3	99.8	GSM270868	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
48.7	99.8	GSM270870	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
34.4	99.7	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
33.9	99.7	GSM265474	Arabidopsis, whole roots, -Fe, 72 hour, rep 2	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
30.6	99.7	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.6	99.7	GSM265473	Arabidopsis, whole roots, -Fe, 72 hour, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
26.0	99.7	GSM133293	NO.30	GSE5698	AtGenExpress: Cytokinin treatment of seedlings
25.4	99.6	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.7	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.5	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.1	99.6	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
22.3	99.6	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.0	99.6	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.8	99.6	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.5	99.6	E-ATMX-13-raw-cel-1556149919
20.9	99.6	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.6	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
20.2	99.6	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.9	99.6	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
19.5	99.6	GSM265471	Arabidopsis, whole roots, -Fe, 48 hour, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
19.0	99.5	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.2	99.5	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.1	99.5	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.0	99.5	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.0	99.5	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.9	99.5	GSM142902	WW001_ATH1_A1-WILLA-CON	GSE6181	Assembly of the cell wall pectic matrix.
17.8	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.1	99.5	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.8	99.5	GSM125254	Seedling_OEA3L5_rep1	GSE5465	Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
16.3	99.5	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.1	99.4	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.6	99.4	GSM131160	AtGen_C-10_1-Pi-6_REP1_ATH1	GSE5616	AtGenExpress: Response to Phytophthora infestans
14.6	99.4	GSM131161	AtGen_C-11_2-Pi-6_REP2_ATH1	GSE5616	AtGenExpress: Response to Phytophthora infestans
13.9	99.4	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.8	99.4	E-ATMX-13-raw-cel-1556149807
13.4	99.4	GSM184151	ATR1_OE_rep2	GSE7570	ATR1_like_Clade_OE_and_miR
13.3	99.4	GSM125255	Seedling_OEA3L5_rep2	GSE5465	Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
12.9	99.3	GSM131162	AtGen_C-12_3-Pi-6_REP3_ATH1	GSE5616	AtGenExpress: Response to Phytophthora infestans
12.8	99.3	GSM125256	Seedling_OETOP6B_rep1	GSE5465	Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
12.8	99.3	GSM265472	Arabidopsis, whole roots, -Fe, 48 hour, rep 2	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
11.2	99.2	E-ATMX-13-raw-cel-1556149871
11.1	99.2	GSM142904	WW002_ATH1_A1-willa-CON-REP2	GSE6181	Assembly of the cell wall pectic matrix.
11.0	99.2	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.0	99.2	E-ATMX-13-raw-cel-1556149759
9.9	99.1	GSM131164	AtGen_C-14_2-Pi-12_REP2_ATH1	GSE5616	AtGenExpress: Response to Phytophthora infestans
8.8	99.0	GSM125257	Seedling_OETOP6B_rep2	GSE5465	Gene expression in wild-type and transgenic plants overexpressing rice topoisomerase6 genes
8.8	99.0	E-NASC-76-raw-cel-1359879158
8.7	99.0	GSM183513	MYB29_OE_rep1	GSE7570	ATR1_like_Clade_OE_and_miR
8.6	99.0	E-MEXP-807-raw-cel-1173272921

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.015 1 GO:0045087 Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.015	1	GO:0045087	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

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	At3g16600
Gene name	SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing protein
Module size	5 genes
NF	0.18
%ile	15.4

Co-expression analysis

Gene ID At3g16600 Gene name SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing protein Module size 5 genes NF 0.18 %ile 15.4

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 AmiGO0.0151GO:0045087Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

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 At3g16600

Gene name SNF2 domain-containing protein / helicase domain-containing protein / RING finger domain-containing protein

Module size 5 genes

NF 0.18

%ile 15.4

: 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
0.015 1 GO:0045087 Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.

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