CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g42830

Gene name SHP2 (SHATTERPROOF 2)

Module size 5 genes

NF 0.43

%ile 60.2

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
0.15 7.8 1.00 At2g42830 818883 SHP2 (SHATTERPROOF 2) AGAMOUS [AG]-like MADS box protein (AGL5) involved in fruit development (valve margin and dehiscence zone differentiation). A putative direct target of AG. SHP2 has been shown to be a downstream gene of the complex formed by AG and SEP proteins (SEP4 alone does not form a functional complex with AG). O.I. H.G. S.X.
0.86 93.1 0.76 At2g38900 818474 serine protease inhibitor, potato inhibitor I-type family protein Predicted to encode a PR (pathogenesis-related) peptide that belongs to the PR-6 proteinase inhibitor family. Six putative PR-6-type protein encoding genes are found in Arabidopsis: At2g38900, At2g38870, At5g43570, At5g43580, At3g50020 and At3g46860. O.I. H.G. S.X.
0.67 81.6 0.66 At4g15750 827253 invertase/pectin methylesterase inhibitor family protein F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;PO O.I. H.G. S.X.
0.67 81.6 0.63 At5g47350 834782 palmitoyl protein thioesterase family protein F:palmitoyl-(protein) hydrolase activity;P:protein modification process;C:endomembrane system;MPFO O.I. H.G. S.X.
0.50 65.3 0.72 At3g49270 824088 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MPO O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.15	7.8	1.00	At2g42830	818883	SHP2 (SHATTERPROOF 2)	AGAMOUS [AG]-like MADS box protein (AGL5) involved in fruit development (valve margin and dehiscence zone differentiation). A putative direct target of AG. SHP2 has been shown to be a downstream gene of the complex formed by AG and SEP proteins (SEP4 alone does not form a functional complex with AG).	O.I.	H.G.	S.X.
0.86	93.1	0.76	At2g38900	818474	serine protease inhibitor, potato inhibitor I-type family protein	Predicted to encode a PR (pathogenesis-related) peptide that belongs to the PR-6 proteinase inhibitor family. Six putative PR-6-type protein encoding genes are found in Arabidopsis: At2g38900, At2g38870, At5g43570, At5g43580, At3g50020 and At3g46860.	O.I.	H.G.	S.X.
0.67	81.6	0.66	At4g15750	827253	invertase/pectin methylesterase inhibitor family protein	F:enzyme inhibitor activity, pectinesterase inhibitor activity, pectinesterase activity;P:biological_process unknown;C:endomembrane system;PO	O.I.	H.G.	S.X.
0.67	81.6	0.63	At5g47350	834782	palmitoyl protein thioesterase family protein	F:palmitoyl-(protein) hydrolase activity;P:protein modification process;C:endomembrane system;MPFO	O.I.	H.G.	S.X.
0.50	65.3	0.72	At3g49270	824088	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;MPO	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
157.8 99.9 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
120.9 99.9 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
103.2 99.9 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
94.6 99.9 E-MEXP-1344-raw-cel-1559561563
77.9 99.9 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
71.7 99.9 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
69.9 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
67.2 99.8 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
60.2 99.8 E-MEXP-1345-raw-cel-1559561199
57.2 99.8 E-MEXP-1345-raw-cel-1559561139
56.3 99.8 E-MEXP-1344-raw-cel-1559561593
50.8 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.3 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.3 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.0 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.0 99.8 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
43.5 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
42.2 99.8 E-MEXP-1344-raw-cel-1559561683
41.1 99.8 E-MEXP-1344-raw-cel-1559561653
40.9 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.9 99.8 E-MEXP-1345-raw-cel-1559561169
40.8 99.8 E-MEXP-1345-raw-cel-1559561229
40.2 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.2 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.1 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.7 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.9 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
37.8 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
37.6 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.7 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.4 99.7 E-MEXP-1345-raw-cel-1559561259
34.5 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.9 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.7 99.7 E-MEXP-1345-raw-cel-1559561289
32.5 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.4 99.7 E-MEXP-1344-raw-cel-1559561713
27.2 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.9 99.6 E-MEXP-1344-raw-cel-1559561623
21.6 99.6 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.3 99.4 GSM265431 Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.8 99.3 GSM133985 Birnbaum_1-15_StageIII-4_Rep4_ATH1 GSE5749 A gene expression map of the Arabidopsis root
10.0 99.2 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

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
157.8	99.9	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
120.9	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
103.2	99.9	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
94.6	99.9	E-MEXP-1344-raw-cel-1559561563
77.9	99.9	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
71.7	99.9	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
69.9	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
67.2	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
60.2	99.8	E-MEXP-1345-raw-cel-1559561199
57.2	99.8	E-MEXP-1345-raw-cel-1559561139
56.3	99.8	E-MEXP-1344-raw-cel-1559561593
50.8	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.3	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
47.3	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
45.0	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.0	99.8	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
43.5	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
42.2	99.8	E-MEXP-1344-raw-cel-1559561683
41.1	99.8	E-MEXP-1344-raw-cel-1559561653
40.9	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
40.9	99.8	E-MEXP-1345-raw-cel-1559561169
40.8	99.8	E-MEXP-1345-raw-cel-1559561229
40.2	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.2	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.1	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.7	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.9	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
37.8	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
37.6	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.7	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.4	99.7	E-MEXP-1345-raw-cel-1559561259
34.5	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.9	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.7	99.7	E-MEXP-1345-raw-cel-1559561289
32.5	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.4	99.7	E-MEXP-1344-raw-cel-1559561713
27.2	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
22.9	99.6	E-MEXP-1344-raw-cel-1559561623
21.6	99.6	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.3	99.4	GSM265431	Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.8	99.3	GSM133985	Birnbaum_1-15_StageIII-4_Rep4_ATH1	GSE5749	A gene expression map of the Arabidopsis root
10.0	99.2	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

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.100 1 GO:0048440 The process whose specific outcome is the progression of the carpel over time, from its formation to the mature structure. A carpel is an organ (generally believed to be a modified foliar unit) at the centre of a flower, bearing one or more ovules and having its margins fused together or with other carpels to enclose the ovule in an ovary, and consisting also of a stigma and usually a style.
0.061 1 GO:0048481 The process whose specific outcome is the progression of the ovule over time, from its formation to the mature structure. The ovule is the structure in seed plants enclosing the female gametophyte, and is composed of the nucellus, one or two integuments, and the funiculus; it develops into the seed.
0.019 1 GO:0006464 The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).

SF	Genes	GO ID	Process Name
0.100	1	GO:0048440	The process whose specific outcome is the progression of the carpel over time, from its formation to the mature structure. A carpel is an organ (generally believed to be a modified foliar unit) at the centre of a flower, bearing one or more ovules and having its margins fused together or with other carpels to enclose the ovule in an ovary, and consisting also of a stigma and usually a style.
0.061	1	GO:0048481	The process whose specific outcome is the progression of the ovule over time, from its formation to the mature structure. The ovule is the structure in seed plants enclosing the female gametophyte, and is composed of the nucellus, one or two integuments, and the funiculus; it develops into the seed.
0.019	1	GO:0006464	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).

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	At2g42830
Gene name	SHP2 (SHATTERPROOF 2)
Module size	5 genes
NF	0.43
%ile	60.2

Co-expression analysis

Gene ID At2g42830 Gene name SHP2 (SHATTERPROOF 2) Module size 5 genes NF 0.43 %ile 60.2

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 At2g42830

Gene name SHP2 (SHATTERPROOF 2)

Module size 5 genes

NF 0.43

%ile 60.2

: 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