CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At4g31550

Gene name WRKY11

Module size 5 genes

NF 0.54

%ile 75.2

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
0.33 38.1 1.00 At4g31550 829282 WRKY11 member of WRKY Transcription Factor; Group II-d; negative regulator of basal resistance to Pseudomonas syringae. O.I. H.G. S.X.
0.86 93.1 0.83 At1g16130 838182 WAKL2 (wall associated kinase-like 2) wall-associated kinase like O.I. H.G. S.X.
0.75 86.9 0.85 At2g27660 817312 DC1 domain-containing protein F:zinc ion binding;P:unknown;C:chloroplast;BPMOFVA O.I. H.G. S.X.
0.55 70.6 0.81 At2g35930 818166 PUB23 (PLANT U-BOX 23) Encodes a cytoplasmically localized U-box domain containing E3 ubiquitin ligase that is involved in the response to water stress and acts as a negative regulator of PAMP-triggered immunity. O.I. H.G. S.X.
0.43 55.3 0.82 At4g23190 828418 CRK11 (CYSTEINE-RICH RLK11) Encodes putative receptor-like protein kinase that is induced by the soil-borne vascular bacteria, Ralstonia solanacearum. Naming convention from Chen et al 2003 (PMID 14756307) O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.33	38.1	1.00	At4g31550	829282	WRKY11	member of WRKY Transcription Factor; Group II-d; negative regulator of basal resistance to Pseudomonas syringae.	O.I.	H.G.	S.X.
0.86	93.1	0.83	At1g16130	838182	WAKL2 (wall associated kinase-like 2)	wall-associated kinase like	O.I.	H.G.	S.X.
0.75	86.9	0.85	At2g27660	817312	DC1 domain-containing protein	F:zinc ion binding;P:unknown;C:chloroplast;BPMOFVA	O.I.	H.G.	S.X.
0.55	70.6	0.81	At2g35930	818166	PUB23 (PLANT U-BOX 23)	Encodes a cytoplasmically localized U-box domain containing E3 ubiquitin ligase that is involved in the response to water stress and acts as a negative regulator of PAMP-triggered immunity.	O.I.	H.G.	S.X.
0.43	55.3	0.82	At4g23190	828418	CRK11 (CYSTEINE-RICH RLK11)	Encodes putative receptor-like protein kinase that is induced by the soil-borne vascular bacteria, Ralstonia solanacearum. Naming convention from Chen et al 2003 (PMID 14756307)	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
154.1 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
124.9 99.9 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
122.0 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
121.8 99.9 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
120.2 99.9 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
116.5 99.9 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
112.4 99.9 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
110.1 99.9 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
108.5 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
100.1 99.9 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
100.1 99.9 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
96.6 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
96.4 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
94.4 99.9 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
92.8 99.9 E-MEXP-807-raw-cel-1173273252
91.2 99.9 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
91.0 99.9 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
85.6 99.9 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
76.4 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
59.7 99.8 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
48.5 99.8 E-MEXP-807-raw-cel-1173273144
39.8 99.8 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
31.3 99.7 GSM189112 HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_1 GSE7796 Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels
24.0 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
21.3 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
20.0 99.6 GSM39212 RRE2_Chitin2 GSE2169 rre1 and rre2 mutants
19.8 99.6 GSM131321 AtGen_6-3421_Saltstress-Roots-6.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
19.0 99.5 GSM133945 Murray_2-1_T0-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
16.7 99.5 GSM39195 RRE1_Chitin1 GSE2169 rre1 and rre2 mutants
16.4 99.5 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.4 99.5 GSM39213 RRE2_Chitin3 GSE2169 rre1 and rre2 mutants
16.1 99.5 E-NASC-76-raw-cel-1359879132
15.4 99.5 GSM39211 RRE2_Chitin1 GSE2169 rre1 and rre2 mutants
15.3 99.4 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
14.9 99.4 GSM39197 RRE1_Chitin3 GSE2169 rre1 and rre2 mutants
14.6 99.4 GSM266662 Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 1 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
14.1 99.4 GSM13784 Cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
13.7 99.4 GSM131322 AtGen_6-3422_Saltstress-Roots-6.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
12.2 99.3 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
12.0 99.3 GSM133947 Murray_2-3_T4-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
10.8 99.2 GSM39205 Col_Chitin3 GSE2169 rre1 and rre2 mutants
10.8 99.2 GSM133950 Murray_2-6_T10-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
10.5 99.2 GSM184909 Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3 GSE7641 Expression analysis of root cell-types after treatment with salt
10.5 99.2 GSM13783 Dexamethasone plus cycloheximide - replicate GSE911 Identification of LEAFY targets during reproductive transition
10.4 99.2 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
10.2 99.2 GSM184907 Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
9.8 99.1 GSM39214 RRE2_Chitin4 GSE2169 rre1 and rre2 mutants
9.3 99.1 GSM266664 Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 3 GSE10501 Expression analysis of root cell-types after iron deficiency (-Fe) treatment
9.3 99.1 E-ATMX-33-raw-cel-1562596174
9.1 99.1 GSM39204 Col_Chitin2 GSE2169 rre1 and rre2 mutants
9.0 99.1 GSM39196 RRE1_Chitin2 GSE2169 rre1 and rre2 mutants
8.7 99.0 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.6 99.0 GSM258003 LMPC-derived phloem_2 GSE10247 Transcriptome analysis of the Arabidopsis phloem

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
154.1	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
124.9	99.9	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
122.0	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
121.8	99.9	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
120.2	99.9	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
116.5	99.9	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
112.4	99.9	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
110.1	99.9	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
108.5	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
100.1	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
100.1	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
96.6	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
96.4	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
94.4	99.9	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
92.8	99.9	E-MEXP-807-raw-cel-1173273252
91.2	99.9	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
91.0	99.9	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
85.6	99.9	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
76.4	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
59.7	99.8	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
48.5	99.8	E-MEXP-807-raw-cel-1173273144
39.8	99.8	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
31.3	99.7	GSM189112	HSP90_Reduced_RNAi-A3_Biological_Replicate_2_Technical_Replicate_1	GSE7796	Phenotypic Diversity and Altered Environmental Plasticity in Arabidopsis thaliana with Reduced HSP90 Levels
24.0	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
21.3	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
20.0	99.6	GSM39212	RRE2_Chitin2	GSE2169	rre1 and rre2 mutants
19.8	99.6	GSM131321	AtGen_6-3421_Saltstress-Roots-6.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
19.0	99.5	GSM133945	Murray_2-1_T0-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
16.7	99.5	GSM39195	RRE1_Chitin1	GSE2169	rre1 and rre2 mutants
16.4	99.5	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
16.4	99.5	GSM39213	RRE2_Chitin3	GSE2169	rre1 and rre2 mutants
16.1	99.5	E-NASC-76-raw-cel-1359879132
15.4	99.5	GSM39211	RRE2_Chitin1	GSE2169	rre1 and rre2 mutants
15.3	99.4	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
14.9	99.4	GSM39197	RRE1_Chitin3	GSE2169	rre1 and rre2 mutants
14.6	99.4	GSM266662	Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 1	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
14.1	99.4	GSM13784	Cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
13.7	99.4	GSM131322	AtGen_6-3422_Saltstress-Roots-6.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
12.2	99.3	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
12.0	99.3	GSM133947	Murray_2-3_T4-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
10.8	99.2	GSM39205	Col_Chitin3	GSE2169	rre1 and rre2 mutants
10.8	99.2	GSM133950	Murray_2-6_T10-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
10.5	99.2	GSM184909	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3	GSE7641	Expression analysis of root cell-types after treatment with salt
10.5	99.2	GSM13783	Dexamethasone plus cycloheximide - replicate	GSE911	Identification of LEAFY targets during reproductive transition
10.4	99.2	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
10.2	99.2	GSM184907	Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
9.8	99.1	GSM39214	RRE2_Chitin4	GSE2169	rre1 and rre2 mutants
9.3	99.1	GSM266664	Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 3	GSE10501	Expression analysis of root cell-types after iron deficiency (-Fe) treatment
9.3	99.1	E-ATMX-33-raw-cel-1562596174
9.1	99.1	GSM39204	Col_Chitin2	GSE2169	rre1 and rre2 mutants
9.0	99.1	GSM39196	RRE1_Chitin2	GSE2169	rre1 and rre2 mutants
8.7	99.0	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.6	99.0	GSM258003	LMPC-derived phloem_2	GSE10247	Transcriptome analysis of the Arabidopsis phloem

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.222 1 GO:0002679 A phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
0.222 1 GO:0051865 The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
0.065 1 GO:0009816 A response of an organism to a bacterium that prevents the occurrence or spread of disease.

SF	Genes	GO ID	Process Name
0.222	1	GO:0002679	A phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
0.222	1	GO:0051865	The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
0.065	1	GO:0009816	A response of an organism to a bacterium that prevents the occurrence or spread of disease.

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

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Gene ID	At4g31550
Gene name	WRKY11
Module size	5 genes
NF	0.54
%ile	75.2

Co-expression analysis

Gene ID At4g31550 Gene name WRKY11 Module size 5 genes NF 0.54 %ile 75.2

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 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 At4g31550

Gene name WRKY11

Module size 5 genes

NF 0.54

%ile 75.2

: 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

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