CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g29190

Gene name lyase/ magnesium ion binding

Module size 24 genes

NF 0.52

%ile 73.5

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 At3g29190 822572 lyase/ magnesium ion binding F:lyase activity, magnesium ion binding;P:metabolic process;C:unknown;POB O.I. H.G. S.X.
0.68 82.2 0.84 At4g03850 3770317 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.67 81.6 0.83 At3g42330 823226 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.67 81.6 0.84 At3g42730 823306 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.63 78.1 0.85 At1g41770 840783 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.63 78.1 0.83 At5g35010 833446 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.59 74.7 0.83 At4g08000 3769934 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.57 73.8 0.83 At3g55650 824731 pyruvate kinase, putative F:pyruvate kinase activity, potassium ion binding, magnesium ion binding, catalytic activity;P:glycolysis;C:mitochondrion;BOMPFA O.I. H.G. S.X.
0.56 73.0 0.85 At5g34970 833442 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.56 73.0 0.84 At3g32000 3769220 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.54 69.5 0.84 At2g10880 3768614 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.53 68.6 0.85 At2g06160 3767898 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.52 67.4 0.84 At1g37160 3767064 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.52 67.4 0.84 At2g14010 815885 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.47 61.2 0.84 At1g40150 3767174 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.46 59.8 0.83 At2g07701 815376 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.45 58.3 0.84 At4g07360 3770409 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.44 57.2 0.84 At2g10140 3767931 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.43 55.3 0.83 At1g33860 840283 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown O.I. H.G. S.X.
0.43 55.3 0.85 At4g04050 3770301 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.40 50.8 0.82 At1g12935 3766713 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.39 48.4 0.85 At1g42360 3767241 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.38 46.7 0.82 At4g08890 3769919 transposable element gene F:unknown;P:unknown;C:unknown O.I. H.G. S.X.
0.32 35.7 0.83 At2g07395 3768424 transposable element gene F:unknown;P:unknown;C:unknown 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	At3g29190	822572	lyase/ magnesium ion binding	F:lyase activity, magnesium ion binding;P:metabolic process;C:unknown;POB	O.I.	H.G.	S.X.
0.68	82.2	0.84	At4g03850	3770317	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.67	81.6	0.83	At3g42330	823226	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.67	81.6	0.84	At3g42730	823306	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.63	78.1	0.85	At1g41770	840783	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.63	78.1	0.83	At5g35010	833446	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.59	74.7	0.83	At4g08000	3769934	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.57	73.8	0.83	At3g55650	824731	pyruvate kinase, putative	F:pyruvate kinase activity, potassium ion binding, magnesium ion binding, catalytic activity;P:glycolysis;C:mitochondrion;BOMPFA	O.I.	H.G.	S.X.
0.56	73.0	0.85	At5g34970	833442	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.56	73.0	0.84	At3g32000	3769220	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.54	69.5	0.84	At2g10880	3768614	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.53	68.6	0.85	At2g06160	3767898	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.52	67.4	0.84	At1g37160	3767064	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.52	67.4	0.84	At2g14010	815885	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.47	61.2	0.84	At1g40150	3767174	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.46	59.8	0.83	At2g07701	815376	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.45	58.3	0.84	At4g07360	3770409	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.44	57.2	0.84	At2g10140	3767931	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.43	55.3	0.83	At1g33860	840283	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown	O.I.	H.G.	S.X.
0.43	55.3	0.85	At4g04050	3770301	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.40	50.8	0.82	At1g12935	3766713	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.39	48.4	0.85	At1g42360	3767241	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.38	46.7	0.82	At4g08890	3769919	transposable element gene	F:unknown;P:unknown;C:unknown	O.I.	H.G.	S.X.
0.32	35.7	0.83	At2g07395	3768424	transposable element gene	F:unknown;P:unknown;C:unknown	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
76.9 99.9 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
51.2 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.3 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.1 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.5 99.7 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.3 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
34.1 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.8 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.6 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
32.5 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.5 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.2 99.7 GSM133775 Lindsey_1-27_torpedo-meristem_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
32.2 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.1 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
29.3 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
29.1 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
28.8 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.6 99.7 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
28.3 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.9 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.0 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.8 99.6 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.8 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
24.3 99.6 GSM133765 Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
20.7 99.6 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.0 99.5 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
14.4 99.4 E-ATMX-33-raw-cel-1562596241
13.4 99.4 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.5 99.1 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.0 99.1 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
76.9	99.9	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
51.2	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.3	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.1	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
36.5	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.3	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
34.1	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.8	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.6	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
32.5	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.5	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.2	99.7	GSM133775	Lindsey_1-27_torpedo-meristem_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
32.2	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.1	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
29.3	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
29.1	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
28.8	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.6	99.7	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
28.3	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
26.9	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.0	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.8	99.6	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.8	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
24.3	99.6	GSM133765	Lindsey_1-17_torpedo-cotyledon_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
20.7	99.6	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
17.0	99.5	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
14.4	99.4	E-ATMX-33-raw-cel-1562596241
13.4	99.4	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.5	99.1	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.0	99.1	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.029 1 GO:0006096 The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.029	1	GO:0006096	The chemical reactions and pathways resulting in the breakdown of a monosaccharide (generally glucose) into pyruvate, with the concomitant production of a small amount of ATP. Pyruvate may be converted to ethanol, lactate, or other small molecules, or fed into the TCA cycle.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.022 1 00620 Pyruvate metabolism
0.020 1 00710 Carbon fixation in photosynthetic organisms
0.018 1 00010 Glycolysis / Gluconeogenesis

SF	Genes	KEGG ID	Pathway name
0.022	1	00620	Pyruvate metabolism
0.020	1	00710	Carbon fixation in photosynthetic organisms
0.018	1	00010	Glycolysis / Gluconeogenesis

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	At3g29190
Gene name	lyase/ magnesium ion binding
Module size	24 genes
NF	0.52
%ile	73.5

Co-expression analysis

Gene ID At3g29190 Gene name lyase/ magnesium ion binding Module size 24 genes NF 0.52 %ile 73.5

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 KEGG0.022100620Pyruvate metabolism0.020100710Carbon fixation in photosynthetic organisms0.018100010Glycolysis / Gluconeogenesis

Inter-species module comparison

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

Gene ID At3g29190

Gene name lyase/ magnesium ion binding

Module size 24 genes

NF 0.52

%ile 73.5

: 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
0.022 1 00620 Pyruvate metabolism
0.020 1 00710 Carbon fixation in photosynthetic organisms
0.018 1 00010 Glycolysis / Gluconeogenesis

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