CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g48070

Gene name XTH20 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 20)

Module size 5 genes

NF 0.24

%ile 24.8

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
0.40 50.8 1.00 At5g48070 834859 XTH20 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 20) putative xyloglucan endotransglycosylase/hydrolase, expressed primarily in the stele of mature non-elongating regions of both the main and the lateral root. Is expressed in lateral root primordia but expression ceases after lateral root begins to grow. O.I. H.G. S.X.
0.33 38.1 0.76 At4g13235 826940 EDA21 (embryo sac development arrest 21) Encodes a defensin-like (DEFL) family protein. O.I. H.G. S.X.
0.33 38.1 0.67 At4g36430 829795 peroxidase, putative F:electron carrier activity, peroxidase activity, heme binding;P:response to other organism;C:cell wall;PFOBM O.I. H.G. S.X.
0.22 17.5 0.66 At3g13650 820569 disease resistance response F:molecular_function unknown;P:lignan biosynthetic process, defense response;C:endomembrane system;P O.I. H.G. S.X.
0.13 5.8 0.62 At4g22212 828313 - Encodes a defensin-like (DEFL) family protein. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.40	50.8	1.00	At5g48070	834859	XTH20 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 20)	putative xyloglucan endotransglycosylase/hydrolase, expressed primarily in the stele of mature non-elongating regions of both the main and the lateral root. Is expressed in lateral root primordia but expression ceases after lateral root begins to grow.	O.I.	H.G.	S.X.
0.33	38.1	0.76	At4g13235	826940	EDA21 (embryo sac development arrest 21)	Encodes a defensin-like (DEFL) family protein.	O.I.	H.G.	S.X.
0.33	38.1	0.67	At4g36430	829795	peroxidase, putative	F:electron carrier activity, peroxidase activity, heme binding;P:response to other organism;C:cell wall;PFOBM	O.I.	H.G.	S.X.
0.22	17.5	0.66	At3g13650	820569	disease resistance response	F:molecular_function unknown;P:lignan biosynthetic process, defense response;C:endomembrane system;P	O.I.	H.G.	S.X.
0.13	5.8	0.62	At4g22212	828313	-	Encodes a defensin-like (DEFL) family protein.	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
188.2 100.0 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
187.6 100.0 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
177.8 100.0 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
172.1 100.0 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
113.7 99.9 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
107.9 99.9 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
107.0 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
93.7 99.9 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
92.4 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
87.3 99.9 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
81.8 99.9 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
79.8 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
78.2 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
74.9 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
62.1 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
61.1 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.9 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
55.1 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
49.7 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.3 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.3 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
44.9 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.5 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.6 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
36.9 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
34.0 99.7 GSM133758 Lindsey_1-11_heart-stage-root_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
30.1 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.4 99.6 GSM176878 AWP_AL_Txed_2 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
16.9 99.5 GSM176879 AWP_Control_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
15.5 99.5 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
13.4 99.4 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
11.5 99.3 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
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
9.0 99.1 GSM133760 Lindsey_1-12_heart-stage-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
188.2	100.0	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
187.6	100.0	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
177.8	100.0	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
172.1	100.0	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
113.7	99.9	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
107.9	99.9	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
107.0	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
93.7	99.9	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
92.4	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
87.3	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
81.8	99.9	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
79.8	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
78.2	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
74.9	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.1	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
61.1	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
56.9	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
55.1	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
49.7	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.3	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.3	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
44.9	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.5	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.6	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
36.9	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
34.0	99.7	GSM133758	Lindsey_1-11_heart-stage-root_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
30.1	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.4	99.6	GSM176878	AWP_AL_Txed_2	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
16.9	99.5	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
15.5	99.5	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
13.4	99.4	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
11.5	99.3	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
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
9.0	99.1	GSM133760	Lindsey_1-12_heart-stage-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.095 1 GO:0009807 The chemical reactions and pathways resulting in the formation of lignans, any member of a class of plant metabolites related to lignins. Lignans are usually found as phenylpropanoid dimers in which the phenylpropanoid units are linked tail to tail and thus having a 2,3 dibenzylbutane skeleton, but higher oligomers can also exist.
0.074 1 GO:0006073 The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
0.049 1 GO:0009553 The process whose specific outcome is the progression of the embryo sac over time, from its formation to the mature structure. The process begins with the meiosis of the megasporocyte to form four haploid megaspores. Three of the megaspores disintegrate, and the fourth undergoes mitosis giving rise to a binucleate syncytial embryo sac. The two haploid nuclei migrate to the opposite poles of the embryo sac and then undergo two rounds of mitosis generating four haploid nuclei at each pole. One nucleus from each set of four migrates to the center of the cell. Cellularization occurs, resulting in an eight-nucleate seven-celled structure. This structure contains two synergid cells and an egg cell at the micropylar end, and three antipodal cells at the other end. A binucleate endosperm mother cell is formed at the center. The two polar nuclei fuse resulting in a mononucleate diploid endosperm mother cell. The three antipodal cells degenerate.

SF	Genes	GO ID	Process Name
0.095	1	GO:0009807	The chemical reactions and pathways resulting in the formation of lignans, any member of a class of plant metabolites related to lignins. Lignans are usually found as phenylpropanoid dimers in which the phenylpropanoid units are linked tail to tail and thus having a 2,3 dibenzylbutane skeleton, but higher oligomers can also exist.
0.074	1	GO:0006073	The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues.
0.049	1	GO:0009553	The process whose specific outcome is the progression of the embryo sac over time, from its formation to the mature structure. The process begins with the meiosis of the megasporocyte to form four haploid megaspores. Three of the megaspores disintegrate, and the fourth undergoes mitosis giving rise to a binucleate syncytial embryo sac. The two haploid nuclei migrate to the opposite poles of the embryo sac and then undergo two rounds of mitosis generating four haploid nuclei at each pole. One nucleus from each set of four migrates to the center of the cell. Cellularization occurs, resulting in an eight-nucleate seven-celled structure. This structure contains two synergid cells and an egg cell at the micropylar end, and three antipodal cells at the other end. A binucleate endosperm mother cell is formed at the center. The two polar nuclei fuse resulting in a mononucleate diploid endosperm mother cell. The three antipodal cells degenerate.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.024 1 00360 Phenylalanine metabolism
0.023 1 00680 Methane metabolism
0.019 1 00940 Phenylpropanoid biosynthesis

SF	Genes	KEGG ID	Pathway name
0.024	1	00360	Phenylalanine metabolism
0.023	1	00680	Methane metabolism
0.019	1	00940	Phenylpropanoid biosynthesis

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

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Gene ID	At5g48070
Gene name	XTH20 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 20)
Module size	5 genes
NF	0.24
%ile	24.8

Co-expression analysis

Gene ID At5g48070 Gene name XTH20 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 20) Module size 5 genes NF 0.24 %ile 24.8

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 KEGG0.024100360Phenylalanine metabolism0.023100680Methane metabolism0.019100940Phenylpropanoid biosynthesis

Inter-species module comparison

Select a plant to compare co-expressed genes between species.Glycine_maxHordeum_vulgareOryza_sativaPopulus_trichocarpaTriticum_aestivumVitis_viniferaZea_mays

Gene ID At5g48070

Gene name XTH20 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE 20)

Module size 5 genes

NF 0.24

%ile 24.8

: 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
0.024 1 00360 Phenylalanine metabolism
0.023 1 00680 Methane metabolism
0.019 1 00940 Phenylpropanoid biosynthesis

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