CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g40020

Gene name pathogenesis-related thaumatin family protein

Module size 5 genes

NF 0.44

%ile 62.8

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 At5g40020 833999 pathogenesis-related thaumatin family protein F:molecular_function unknown;P:response to other organism;C:endomembrane system;PFMBO O.I. H.G. S.X.
0.60 75.7 0.75 At1g08340 837354 rac GTPase activating protein, putative F:Rac GTPase activator activity;P:signal transduction;C:intracellular;MOFPVBA O.I. H.G. S.X.
0.57 73.8 0.80 At3g62020 825375 GLP10 (GERMIN-LIKE PROTEIN 10) germin-like protein (GLP10) O.I. H.G. S.X.
0.40 50.8 0.87 At2g37090 818285 IRX9 (IRREGULAR XYLEM 9) The IRX9 gene encodes a putative family 43 glycosyl transferase. It was coordinately expressed with the cellulose synthase subunits during secondary cell wall formation. Cell wall analysis revealed a decrease in the abundance of xylan in the irx9 mutant, indicating that IRX9 is required for xylan synthesis. Mutants have irregular xylem phenotype suggesting a role in secondary cell wall biosynthesis. O.I. H.G. S.X.
0.40 50.8 0.85 At4g18780 827612 IRX1 (IRREGULAR XYLEM 1) Encodes a member of the cellulose synthase family involved in secondary cell wall biosynthesis. Mutants have abnormal xylem formation, reduced cellulose content, and enhanced drought and osmotic stress tolerance. Mediates resistance towards bacterial pathogens via ABA. Confers resistance towards bacterial and fungal pathogens, independent of salicylic acid, ethylene and jasmonate signaling. 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	At5g40020	833999	pathogenesis-related thaumatin family protein	F:molecular_function unknown;P:response to other organism;C:endomembrane system;PFMBO	O.I.	H.G.	S.X.
0.60	75.7	0.75	At1g08340	837354	rac GTPase activating protein, putative	F:Rac GTPase activator activity;P:signal transduction;C:intracellular;MOFPVBA	O.I.	H.G.	S.X.
0.57	73.8	0.80	At3g62020	825375	GLP10 (GERMIN-LIKE PROTEIN 10)	germin-like protein (GLP10)	O.I.	H.G.	S.X.
0.40	50.8	0.87	At2g37090	818285	IRX9 (IRREGULAR XYLEM 9)	The IRX9 gene encodes a putative family 43 glycosyl transferase. It was coordinately expressed with the cellulose synthase subunits during secondary cell wall formation. Cell wall analysis revealed a decrease in the abundance of xylan in the irx9 mutant, indicating that IRX9 is required for xylan synthesis. Mutants have irregular xylem phenotype suggesting a role in secondary cell wall biosynthesis.	O.I.	H.G.	S.X.
0.40	50.8	0.85	At4g18780	827612	IRX1 (IRREGULAR XYLEM 1)	Encodes a member of the cellulose synthase family involved in secondary cell wall biosynthesis. Mutants have abnormal xylem formation, reduced cellulose content, and enhanced drought and osmotic stress tolerance. Mediates resistance towards bacterial pathogens via ABA. Confers resistance towards bacterial and fungal pathogens, independent of salicylic acid, ethylene and jasmonate signaling.	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
381.5 100.0 GSM154507 Arabidopsis growing pollen tubes rep1 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
304.8 100.0 GSM154508 Arabidopsis growing pollen tubes rep2 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
80.4 99.9 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
80.4 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
74.9 99.9 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
67.6 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.8 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
57.6 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
52.6 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.4 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.8 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.1 99.8 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
48.4 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.8 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.4 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.1 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.0 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.5 99.7 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.8 99.5 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.7 99.5 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
16.8 99.5 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.4 99.5 GSM154506 Arabidopsis hydrated pollen grains rep2 GSE6696 Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
16.1 99.5 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.7 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
12.6 99.3 GSM131637 ATGE_73_B GSE5632 AtGenExpress: Developmental series (flowers and pollen)
11.8 99.3 GSM131638 ATGE_73_C GSE5632 AtGenExpress: Developmental series (flowers and pollen)
10.6 99.2 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.0 99.1 GSM290758 root - 01% oxygen - 48h - A GSE11558 transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
381.5	100.0	GSM154507	Arabidopsis growing pollen tubes rep1	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
304.8	100.0	GSM154508	Arabidopsis growing pollen tubes rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
80.4	99.9	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
80.4	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
74.9	99.9	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
67.6	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
60.8	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
57.6	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.6	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.4	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.8	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.1	99.8	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
48.4	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.8	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.4	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.1	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.0	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.5	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.8	99.5	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.7	99.5	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
16.8	99.5	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.4	99.5	GSM154506	Arabidopsis hydrated pollen grains rep2	GSE6696	Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis
16.1	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.7	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
12.6	99.3	GSM131637	ATGE_73_B	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
11.8	99.3	GSM131638	ATGE_73_C	GSE5632	AtGenExpress: Developmental series (flowers and pollen)
10.6	99.2	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.0	99.1	GSM290758	root - 01% oxygen - 48h - A	GSE11558	transcript profiling of the adaptive response to decreases in oxygen concentration in the roots of Arabidopsis plants

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.286 1 GO:0010116 Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of abscisic acid.
0.286 1 GO:0010413 The chemical reactions and pathways involving xylan, a polymer containing a beta-(1->4)-linked D-xylose backbone decorated with glucuronic acid side units.
0.174 2 GO:0009834 The chemical reactions and pathways resulting in the formation of inextensible cellulose and pectin-containing cell walls that are formed between the plasma membrane and primary cell wall after cell expansion is complete. An example of this is found in Arabidopsis thaliana.

SF	Genes	GO ID	Process Name
0.286	1	GO:0010116	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of abscisic acid.
0.286	1	GO:0010413	The chemical reactions and pathways involving xylan, a polymer containing a beta-(1->4)-linked D-xylose backbone decorated with glucuronic acid side units.
0.174	2	GO:0009834	The chemical reactions and pathways resulting in the formation of inextensible cellulose and pectin-containing cell walls that are formed between the plasma membrane and primary cell wall after cell expansion is complete. An example of this is found in Arabidopsis thaliana.

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	At5g40020
Gene name	pathogenesis-related thaumatin family protein
Module size	5 genes
NF	0.44
%ile	62.8

Co-expression analysis

Gene ID At5g40020 Gene name pathogenesis-related thaumatin family protein Module size 5 genes NF 0.44 %ile 62.8

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 At5g40020

Gene name pathogenesis-related thaumatin family protein

Module size 5 genes

NF 0.44

%ile 62.8

: 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