CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g24670

Gene name pectate lyase family protein

Module size 5 genes

NF 0.80

%ile 94.5

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
1.00 100.0 1.00 At3g24670 822063 pectate lyase family protein F:pectate lyase activity;P:biological_process unknown;C:endomembrane system;PBFO O.I. H.G. S.X.
1.00 100.0 0.83 At4g09990 826590 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POB O.I. H.G. S.X.
0.80 89.8 0.82 At2g47540 819367 pollen Ole e 1 allergen and extensin family protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P O.I. H.G. S.X.
0.80 89.8 0.87 At5g49270 834987 SHV2 (SHAVEN 2) Involved in successfully establishing tip growth in root hairs. O.I. H.G. S.X.
0.57 73.8 0.83 At2g34910 818056 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.
1.00	100.0	1.00	At3g24670	822063	pectate lyase family protein	F:pectate lyase activity;P:biological_process unknown;C:endomembrane system;PBFO	O.I.	H.G.	S.X.
1.00	100.0	0.83	At4g09990	826590	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;POB	O.I.	H.G.	S.X.
0.80	89.8	0.82	At2g47540	819367	pollen Ole e 1 allergen and extensin family protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;P	O.I.	H.G.	S.X.
0.80	89.8	0.87	At5g49270	834987	SHV2 (SHAVEN 2)	Involved in successfully establishing tip growth in root hairs.	O.I.	H.G.	S.X.
0.57	73.8	0.83	At2g34910	818056	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
363.9 100.0 GSM133776 Lindsey_1-1_globular-apical_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
187.2 100.0 GSM133756 Lindsey_1-10_heart-stage-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
159.4 99.9 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
89.1 99.9 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
86.3 99.9 GSM133779 Lindsey_1-5_globular-basal_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
72.3 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
59.9 99.8 GSM10453 WT Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
59.3 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
57.1 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
53.6 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
50.3 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.5 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.3 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.9 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.7 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.4 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.2 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.0 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.2 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.5 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.6 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
27.1 99.7 GSM133768 Lindsey_1-20_torpedo-basal_Rep5_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
18.1 99.5 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.1 99.4 GSM131699 ATGE_81_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
11.4 99.3 GSM133757 Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.6 99.2 GSM131697 ATGE_81_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
10.2 99.2 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.0 99.2 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.1 99.1 GSM176879 AWP_Control_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
363.9	100.0	GSM133776	Lindsey_1-1_globular-apical_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
187.2	100.0	GSM133756	Lindsey_1-10_heart-stage-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
159.4	99.9	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
89.1	99.9	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
86.3	99.9	GSM133779	Lindsey_1-5_globular-basal_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
72.3	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
59.9	99.8	GSM10453	WT Mature Green Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
59.3	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
57.1	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
53.6	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.3	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.5	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.3	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.3	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.9	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.7	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.4	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.2	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.0	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.2	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.8	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.5	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.6	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.1	99.7	GSM133768	Lindsey_1-20_torpedo-basal_Rep5_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
18.1	99.5	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.1	99.4	GSM131699	ATGE_81_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
11.4	99.3	GSM133757	Lindsey_1-8_heart-stage-cotyledon_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.6	99.2	GSM131697	ATGE_81_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
10.2	99.2	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.0	99.2	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.1	99.1	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.143 1 GO:0009932 Growth that occurs specifically at the tip of a cell.
0.125 1 GO:0048765 The process whereby a relatively unspecialized cell acquires specialized features of a root hair cell.
0.118 1 GO:0010053 The process whereby a relatively unspecialized cell in the root epidermis acquires the specialized features of a trichoblast or atrichoblast.

SF	Genes	GO ID	Process Name
0.143	1	GO:0009932	Growth that occurs specifically at the tip of a cell.
0.125	1	GO:0048765	The process whereby a relatively unspecialized cell acquires specialized features of a root hair cell.
0.118	1	GO:0010053	The process whereby a relatively unspecialized cell in the root epidermis acquires the specialized features of a trichoblast or atrichoblast.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.054 1 00040 Pentose and glucuronate interconversions

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.054	1	00040	Pentose and glucuronate interconversions

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	At3g24670
Gene name	pectate lyase family protein
Module size	5 genes
NF	0.80
%ile	94.5

Co-expression analysis

Gene ID At3g24670 Gene name pectate lyase family protein Module size 5 genes NF 0.80 %ile 94.5

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

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.054100040Pentose and glucuronate interconversions

Inter-species module comparison

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

Gene ID At3g24670

Gene name pectate lyase family protein

Module size 5 genes

NF 0.80

%ile 94.5

: 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
0.054 1 00040 Pentose and glucuronate interconversions

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