CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g73310

Gene name scpl4 (serine carboxypeptidase-like 4)

Module size 9 genes

NF 0.23

%ile 23.4

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
0.21 15.8 1.00 At1g73310 843665 scpl4 (serine carboxypeptidase-like 4) F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFBO O.I. H.G. S.X.
0.50 65.3 0.78 At1g35330 840422 zinc finger (C3HC4-type RING finger) family protein F:protein binding, zinc ion binding;P:unknown;C:endomembrane system;PMOFVB O.I. H.G. S.X.
0.37 45.0 0.79 At1g73280 843662 scpl3 (serine carboxypeptidase-like 3) F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFBO O.I. H.G. S.X.
0.30 32.1 0.77 At5g10280 830892 ATMYB92 (MYB DOMAIN PROTEIN 92) Encodes a putative transcription factor (MYB92). O.I. H.G. S.X.
0.20 14.4 0.77 At1g72300 843562 leucine-rich repeat transmembrane protein kinase, putative Encodes a leucine-rich repeat receptor kinase (LRR-RK) involved in the perception of PSY1. PSY1 is an 18-aa tyrosine-sulfated glycopeptide encoded by AT5G58650 that promotes cellular proliferation and expansion. O.I. H.G. S.X.
0.20 14.4 0.77 At2g23960 816929 defense-related protein, putative F:catalytic activity;P:defense response;C:cellular_component unknown;OBAFPM O.I. H.G. S.X.
0.19 12.7 0.77 At4g21230 827872 protein kinase family protein F:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVA O.I. H.G. S.X.
0.16 8.8 0.77 At1g50560 841477 CYP705A25 member of CYP705A O.I. H.G. S.X.
0.16 8.8 0.77 At1g07560 837270 leucine-rich repeat protein kinase, putative F:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;PMOBFVA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.21	15.8	1.00	At1g73310	843665	scpl4 (serine carboxypeptidase-like 4)	F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFBO	O.I.	H.G.	S.X.
0.50	65.3	0.78	At1g35330	840422	zinc finger (C3HC4-type RING finger) family protein	F:protein binding, zinc ion binding;P:unknown;C:endomembrane system;PMOFVB	O.I.	H.G.	S.X.
0.37	45.0	0.79	At1g73280	843662	scpl3 (serine carboxypeptidase-like 3)	F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFBO	O.I.	H.G.	S.X.
0.30	32.1	0.77	At5g10280	830892	ATMYB92 (MYB DOMAIN PROTEIN 92)	Encodes a putative transcription factor (MYB92).	O.I.	H.G.	S.X.
0.20	14.4	0.77	At1g72300	843562	leucine-rich repeat transmembrane protein kinase, putative	Encodes a leucine-rich repeat receptor kinase (LRR-RK) involved in the perception of PSY1. PSY1 is an 18-aa tyrosine-sulfated glycopeptide encoded by AT5G58650 that promotes cellular proliferation and expansion.	O.I.	H.G.	S.X.
0.20	14.4	0.77	At2g23960	816929	defense-related protein, putative	F:catalytic activity;P:defense response;C:cellular_component unknown;OBAFPM	O.I.	H.G.	S.X.
0.19	12.7	0.77	At4g21230	827872	protein kinase family protein	F:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;MPOBFVA	O.I.	H.G.	S.X.
0.16	8.8	0.77	At1g50560	841477	CYP705A25	member of CYP705A	O.I.	H.G.	S.X.
0.16	8.8	0.77	At1g07560	837270	leucine-rich repeat protein kinase, putative	F:kinase activity;P:protein amino acid phosphorylation;C:endomembrane system;PMOBFVA	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
140.2 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
81.0 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
77.8 99.9 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.3 99.9 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.5 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.8 99.8 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
59.6 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.6 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
57.4 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.3 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
55.4 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.6 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.9 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.6 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.7 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
47.6 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
47.1 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.8 99.8 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.9 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.6 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.4 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
40.7 99.8 GSM133760 Lindsey_1-12_heart-stage-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
34.6 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
34.5 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.7 99.7 E-MEXP-98-raw-cel-320188969
29.4 99.7 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.6 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
25.2 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
25.1 99.6 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
24.4 99.6 E-MEXP-98-raw-cel-320188914
23.9 99.6 E-MEXP-1725-raw-cel-1669614582
22.7 99.6 E-MEXP-1725-raw-cel-1669614562
22.4 99.6 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
21.9 99.6 E-MEXP-1725-raw-cel-1669614634
21.5 99.6 GSM131448 AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
21.1 99.6 GSM131447 AtGen_6-9211_Heatstress-Shoots-1.0h_Rep1 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
18.3 99.5 E-MEXP-1725-raw-cel-1669614623
16.0 99.5 GSM131449 AtGen_6-9221_Heatstress-Roots-1.0h_Rep1 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
15.2 99.4 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
14.6 99.4 GSM131453 AtGen_6-9321_Heatstress-Roots-3.0h_Rep1 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
14.5 99.4 GSM131454 AtGen_6-9322_Heatstress-Roots-3.0h_Rep2 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
13.9 99.4 GSM131450 AtGen_6-9222_Heatstress-Roots-1.0h_Rep2 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
13.7 99.4 E-MEXP-98-raw-cel-320188694
12.4 99.3 E-MEXP-98-raw-cel-320188749
12.0 99.3 GSM270870 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
11.5 99.3 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.0 99.2 GSM131451 AtGen_6-9311_Heatstress-Shoots-3.0h_Rep1 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
10.5 99.2 GSM270868 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
10.0 99.2 E-MEXP-509-raw-cel-829148525
9.8 99.1 GSM131452 AtGen_6-9312_Heatstress-Shoots-3.0h_Rep2 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
9.6 99.1 GSM147964 WT Globular Stage Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
9.2 99.1 GSM147963 WT Globular Stage Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
8.6 99.0 GSM184552 Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
140.2	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
81.0	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
77.8	99.9	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
68.3	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
65.5	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.8	99.8	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
59.6	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
58.6	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
57.4	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.3	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
55.4	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.6	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.9	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.6	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.7	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
47.6	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
47.1	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.8	99.8	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.9	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.6	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.4	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
40.7	99.8	GSM133760	Lindsey_1-12_heart-stage-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
34.6	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
34.5	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.7	99.7	E-MEXP-98-raw-cel-320188969
29.4	99.7	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.6	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.2	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.1	99.6	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
24.4	99.6	E-MEXP-98-raw-cel-320188914
23.9	99.6	E-MEXP-1725-raw-cel-1669614582
22.7	99.6	E-MEXP-1725-raw-cel-1669614562
22.4	99.6	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
21.9	99.6	E-MEXP-1725-raw-cel-1669614634
21.5	99.6	GSM131448	AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
21.1	99.6	GSM131447	AtGen_6-9211_Heatstress-Shoots-1.0h_Rep1	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
18.3	99.5	E-MEXP-1725-raw-cel-1669614623
16.0	99.5	GSM131449	AtGen_6-9221_Heatstress-Roots-1.0h_Rep1	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
15.2	99.4	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
14.6	99.4	GSM131453	AtGen_6-9321_Heatstress-Roots-3.0h_Rep1	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
14.5	99.4	GSM131454	AtGen_6-9322_Heatstress-Roots-3.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
13.9	99.4	GSM131450	AtGen_6-9222_Heatstress-Roots-1.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
13.7	99.4	E-MEXP-98-raw-cel-320188694
12.4	99.3	E-MEXP-98-raw-cel-320188749
12.0	99.3	GSM270870	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
11.5	99.3	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.0	99.2	GSM131451	AtGen_6-9311_Heatstress-Shoots-3.0h_Rep1	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
10.5	99.2	GSM270868	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
10.0	99.2	E-MEXP-509-raw-cel-829148525
9.8	99.1	GSM131452	AtGen_6-9312_Heatstress-Shoots-3.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
9.6	99.1	GSM147964	WT Globular Stage Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
9.2	99.1	GSM147963	WT Globular Stage Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
8.6	99.0	GSM184552	Whole roots 2hr KCl control treated then incubated in protoplast-generating solution minus enzymes, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.017 1 GO:0009751 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salicylic acid stimulus.
0.016 1 GO:0009753 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a jasmonic acid stimulus.
0.014 1 GO:0007169 The series of molecular signals generated as a consequence of a transmembrane receptor tyrosine kinase binding to its physiological ligand.

SF	Genes	GO ID	Process Name
0.017	1	GO:0009751	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a salicylic acid stimulus.
0.016	1	GO:0009753	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a jasmonic acid stimulus.
0.014	1	GO:0007169	The series of molecular signals generated as a consequence of a transmembrane receptor tyrosine kinase binding to its physiological ligand.

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

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Gene ID	At1g73310
Gene name	scpl4 (serine carboxypeptidase-like 4)
Module size	9 genes
NF	0.23
%ile	23.4

Co-expression analysis

Gene ID At1g73310 Gene name scpl4 (serine carboxypeptidase-like 4) Module size 9 genes NF 0.23 %ile 23.4

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 At1g73310

Gene name scpl4 (serine carboxypeptidase-like 4)

Module size 9 genes

NF 0.23

%ile 23.4

: 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