CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g08260

Gene name scpl35 (serine carboxypeptidase-like 35)

Module size 5 genes

NF 0.65

%ile 85.6

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
0.50 65.3 1.00 At5g08260 830722 scpl35 (serine carboxypeptidase-like 35) F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFOB O.I. H.G. S.X.
0.75 86.9 0.77 At4g16210 827314 ECHIA (ENOYL-COA HYDRATASE/ISOMERASE A) F:catalytic activity;P:metabolic process;C:peroxisome;BOMFPA O.I. H.G. S.X.
0.75 86.9 0.78 At5g56260 835725 dimethylmenaquinone methyltransferase family protein F:ribonuclease inhibitor activity;P:regulation of RNA metabolic process;C:cellular_component unknown;BOPAFM O.I. H.G. S.X.
0.67 81.6 0.78 At2g22780 816808 PMDH1 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 1) encodes an peroxisomal NAD-malate dehydrogenase that is involved in fatty acid beta-oxidation through providing NAD to the process of converting fatty acyl CoA to acetyl CoA. O.I. H.G. S.X.
0.67 81.6 0.78 At3g06860 819870 MFP2 (MULTIFUNCTIONAL PROTEIN 2) Encodes a multifunctional protein. Involved in peroxisomal fatty acid beta oxidation. Loss-of-function mutant lacks hydroxyacyl-CoA dehydrogenase activity and have reduced levels of long-chain enoyl-CoA hydratase activity. The mutant has fewer but larger peroxisomes. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.50	65.3	1.00	At5g08260	830722	scpl35 (serine carboxypeptidase-like 35)	F:serine-type carboxypeptidase activity;P:proteolysis;C:endomembrane system;PMFOB	O.I.	H.G.	S.X.
0.75	86.9	0.77	At4g16210	827314	ECHIA (ENOYL-COA HYDRATASE/ISOMERASE A)	F:catalytic activity;P:metabolic process;C:peroxisome;BOMFPA	O.I.	H.G.	S.X.
0.75	86.9	0.78	At5g56260	835725	dimethylmenaquinone methyltransferase family protein	F:ribonuclease inhibitor activity;P:regulation of RNA metabolic process;C:cellular_component unknown;BOPAFM	O.I.	H.G.	S.X.
0.67	81.6	0.78	At2g22780	816808	PMDH1 (PEROXISOMAL NAD-MALATE DEHYDROGENASE 1)	encodes an peroxisomal NAD-malate dehydrogenase that is involved in fatty acid beta-oxidation through providing NAD to the process of converting fatty acyl CoA to acetyl CoA.	O.I.	H.G.	S.X.
0.67	81.6	0.78	At3g06860	819870	MFP2 (MULTIFUNCTIONAL PROTEIN 2)	Encodes a multifunctional protein. Involved in peroxisomal fatty acid beta oxidation. Loss-of-function mutant lacks hydroxyacyl-CoA dehydrogenase activity and have reduced levels of long-chain enoyl-CoA hydratase activity. The mutant has fewer but larger peroxisomes.	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
31.9 99.7 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
28.6 99.7 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
24.2 99.6 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
21.7 99.6 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.8 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
20.1 99.6 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.2 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
18.8 99.5 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.5 99.5 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.3 99.5 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.7 99.5 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.5 99.5 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.2 99.5 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.0 99.5 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.5 99.5 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2 99.5 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2 99.5 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.1 99.4 GSM133945 Murray_2-1_T0-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
14.6 99.4 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.2 99.4 GSM265474 Arabidopsis, whole roots, -Fe, 72 hour, rep 2 GSE10502 Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
13.9 99.4 GSM265473 Arabidopsis, whole roots, -Fe, 72 hour, rep 1 GSE10502 Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
13.8 99.4 GSM265472 Arabidopsis, whole roots, -Fe, 48 hour, rep 2 GSE10502 Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
13.4 99.4 GSM265432 Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 1 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.5 99.3 GSM131127 AtGen_B-13_1-6-4_REP1_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
12.2 99.3 GSM265471 Arabidopsis, whole roots, -Fe, 48 hour, rep 1 GSE10502 Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
11.8 99.3 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.3 99.3 GSM131111 AtGen_B-39_3-4-4_REP3_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
11.1 99.2 E-MEXP-711-raw-cel-1563002902
10.6 99.2 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.5 99.2 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8 99.1 E-MEXP-711-raw-cel-1563002839
9.7 99.1 GSM264761 Tween 0.1% 1h GSE10464 Expression data from Arabidopsis thaliana (Ler) rosette leaves treated with paraquat (methyl viologen)
9.5 99.1 GSM131113 AtGen_B-41_3-6-4_REP3_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
9.5 99.1 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 GSM131369 AtGen_6-5321_Genotoxicstress-Roots-3.0h_Rep1 GSE5625 AtGenExpress: Stress Treatments (Genotoxic stress)
8.9 99.0 GSM131139 AtGen_B-25_2-4-4_REP2_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
8.9 99.0 GSM131374 AtGen_6-5422_Genotoxicstress-Roots-6.0h_Rep2 GSE5625 AtGenExpress: Stress Treatments (Genotoxic stress)
8.8 99.0 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.7 99.0 GSM131381 AtGen_6-5621_Genotoxicstress-Roots-24.0h_Rep1 GSE5625 AtGenExpress: Stress Treatments (Genotoxic stress)
8.7 99.0 GSM265430 Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 1 GSE10497 Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
8.6 99.0 GSM131125 AtGen_B-11_1-4-4_REP1_ATH1 GSE5615 AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
31.9	99.7	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
28.6	99.7	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
24.2	99.6	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
21.7	99.6	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
20.8	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
20.1	99.6	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
19.2	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
18.8	99.5	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.5	99.5	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.3	99.5	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.7	99.5	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.5	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
17.2	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.0	99.5	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.5	99.5	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.2	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.1	99.4	GSM133945	Murray_2-1_T0-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
14.6	99.4	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.2	99.4	GSM265474	Arabidopsis, whole roots, -Fe, 72 hour, rep 2	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
13.9	99.4	GSM265473	Arabidopsis, whole roots, -Fe, 72 hour, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
13.8	99.4	GSM265472	Arabidopsis, whole roots, -Fe, 48 hour, rep 2	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
13.4	99.4	GSM265432	Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
12.5	99.3	GSM131127	AtGen_B-13_1-6-4_REP1_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
12.2	99.3	GSM265471	Arabidopsis, whole roots, -Fe, 48 hour, rep 1	GSE10502	Time course expression analysis of the iron deficiency (-Fe) response in Arabidopsis roots
11.8	99.3	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.3	99.3	GSM131111	AtGen_B-39_3-4-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
11.1	99.2	E-MEXP-711-raw-cel-1563002902
10.6	99.2	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.5	99.2	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8	99.1	E-MEXP-711-raw-cel-1563002839
9.7	99.1	GSM264761	Tween 0.1% 1h	GSE10464	Expression data from Arabidopsis thaliana (Ler) rosette leaves treated with paraquat (methyl viologen)
9.5	99.1	GSM131113	AtGen_B-41_3-6-4_REP3_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
9.5	99.1	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4	99.1	GSM131369	AtGen_6-5321_Genotoxicstress-Roots-3.0h_Rep1	GSE5625	AtGenExpress: Stress Treatments (Genotoxic stress)
8.9	99.0	GSM131139	AtGen_B-25_2-4-4_REP2_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors
8.9	99.0	GSM131374	AtGen_6-5422_Genotoxicstress-Roots-6.0h_Rep2	GSE5625	AtGenExpress: Stress Treatments (Genotoxic stress)
8.8	99.0	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.7	99.0	GSM131381	AtGen_6-5621_Genotoxicstress-Roots-24.0h_Rep1	GSE5625	AtGenExpress: Stress Treatments (Genotoxic stress)
8.7	99.0	GSM265430	Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 1	GSE10497	Expression analysis of root developmental zones after iron deficiency (-Fe) treatment
8.6	99.0	GSM131125	AtGen_B-11_1-4-4_REP1_ATH1	GSE5615	AtGenExpress: Response to bacterial-(LPS, HrpZ, Flg22) and oomycete-(NPP1) derived elicitors

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.286 1 GO:0031998 Any process that modulates the frequency, rate or extent of fatty acid bbeta-oxidation.
0.286 1 GO:0080093 Any process that modulates the rate, frequency or extent of photorespiration. Photorespiration is a light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved.
0.250 1 GO:0051252 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.

SF	Genes	GO ID	Process Name
0.286	1	GO:0031998	Any process that modulates the frequency, rate or extent of fatty acid bbeta-oxidation.
0.286	1	GO:0080093	Any process that modulates the rate, frequency or extent of photorespiration. Photorespiration is a light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved.
0.250	1	GO:0051252	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.100 1 00310 Lysine degradation
0.091 1 00410 beta-Alanine metabolism
0.083 1 00640 Propanoate metabolism

SF	Genes	KEGG ID	Pathway name
0.100	1	00310	Lysine degradation
0.091	1	00410	beta-Alanine metabolism
0.083	1	00640	Propanoate metabolism

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	At5g08260
Gene name	scpl35 (serine carboxypeptidase-like 35)
Module size	5 genes
NF	0.65
%ile	85.6

Co-expression analysis

Gene ID At5g08260 Gene name scpl35 (serine carboxypeptidase-like 35) Module size 5 genes NF 0.65 %ile 85.6

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 KEGG0.100100310Lysine degradation0.091100410beta-Alanine metabolism0.083100640Propanoate metabolism

Inter-species module comparison

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

Gene ID At5g08260

Gene name scpl35 (serine carboxypeptidase-like 35)

Module size 5 genes

NF 0.65

%ile 85.6

: 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
0.100 1 00310 Lysine degradation
0.091 1 00410 beta-Alanine metabolism
0.083 1 00640 Propanoate metabolism

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