CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g54540

Gene name -

Module size 16 genes

NF 0.68

%ile 87.5

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
0.54 69.5 1.00 At1g54540 841896 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.86 93.1 0.78 At5g09520 830811 hydroxyproline-rich glycoprotein family protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BMPOFVA O.I. H.G. S.X.
0.81 90.4 0.65 At5g09530 830812 hydroxyproline-rich glycoprotein family protein F:unknown;P:biological_process unknown;C:endomembrane system;MBOPFVA O.I. H.G. S.X.
0.81 90.4 0.69 At2g48140 819426 EDA4 (embryo sac development arrest 4) F:lipid binding;P:megagametogenesis, lipid transport;C:anchored to membrane;PBMOFV O.I. H.G. S.X.
0.80 89.8 0.73 At2g48130 819425 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein F:lipid binding;P:lipid transport;C:anchored to membrane;PBOM O.I. H.G. S.X.
0.80 89.8 0.67 At5g13580 831202 ABC transporter family protein F:ATPase activity, coupled to transmembrane movement of substances;P:response to nematode;C:membrane;BOMAFPV O.I. H.G. S.X.
0.77 88.0 0.75 At4g36610 829813 hydrolase, alpha/beta fold family protein F:hydrolase activity;P:biological_process unknown;C:endomembrane system;BOMPFA O.I. H.G. S.X.
0.77 88.0 0.67 At5g41040 834106 transferase family protein F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFBO O.I. H.G. S.X.
0.71 84.2 0.64 At2g43390 818940 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.69 82.9 0.68 At1g68850 843218 peroxidase, putative F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:endomembrane system;PFOBM O.I. H.G. S.X.
0.69 82.9 0.75 At1g74460 843787 GDSL-motif lipase/hydrolase family protein F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBFOM O.I. H.G. S.X.
0.67 81.6 0.76 At1g56320 842085 unknown protein F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;P O.I. H.G. S.X.
0.65 79.6 0.91 At5g13900 831237 protease inhibitor/seed storage/lipid transfer protein (LTP) family protein F:lipid binding;P:lipid transport;C:anchored to membrane;P O.I. H.G. S.X.
0.59 74.7 0.62 At4g38080 829964 hydroxyproline-rich glycoprotein family protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PMOVBFA O.I. H.G. S.X.
0.51 66.3 0.65 At2g23540 816886 GDSL-motif lipase/hydrolase family protein F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBFOM O.I. H.G. S.X.
0.47 61.2 0.61 At4g20390 827787 integral membrane family protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.54	69.5	1.00	At1g54540	841896	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.86	93.1	0.78	At5g09520	830811	hydroxyproline-rich glycoprotein family protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;BMPOFVA	O.I.	H.G.	S.X.
0.81	90.4	0.65	At5g09530	830812	hydroxyproline-rich glycoprotein family protein	F:unknown;P:biological_process unknown;C:endomembrane system;MBOPFVA	O.I.	H.G.	S.X.
0.81	90.4	0.69	At2g48140	819426	EDA4 (embryo sac development arrest 4)	F:lipid binding;P:megagametogenesis, lipid transport;C:anchored to membrane;PBMOFV	O.I.	H.G.	S.X.
0.80	89.8	0.73	At2g48130	819425	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	F:lipid binding;P:lipid transport;C:anchored to membrane;PBOM	O.I.	H.G.	S.X.
0.80	89.8	0.67	At5g13580	831202	ABC transporter family protein	F:ATPase activity, coupled to transmembrane movement of substances;P:response to nematode;C:membrane;BOMAFPV	O.I.	H.G.	S.X.
0.77	88.0	0.75	At4g36610	829813	hydrolase, alpha/beta fold family protein	F:hydrolase activity;P:biological_process unknown;C:endomembrane system;BOMPFA	O.I.	H.G.	S.X.
0.77	88.0	0.67	At5g41040	834106	transferase family protein	F:transferase activity, transferring acyl groups other than amino-acyl groups, transferase activity;P:biological_process unknown;C:cellular_component unknown;PFBO	O.I.	H.G.	S.X.
0.71	84.2	0.64	At2g43390	818940	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.69	82.9	0.68	At1g68850	843218	peroxidase, putative	F:electron carrier activity, peroxidase activity, heme binding;P:response to oxidative stress;C:endomembrane system;PFOBM	O.I.	H.G.	S.X.
0.69	82.9	0.75	At1g74460	843787	GDSL-motif lipase/hydrolase family protein	F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBFOM	O.I.	H.G.	S.X.
0.67	81.6	0.76	At1g56320	842085	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;P	O.I.	H.G.	S.X.
0.65	79.6	0.91	At5g13900	831237	protease inhibitor/seed storage/lipid transfer protein (LTP) family protein	F:lipid binding;P:lipid transport;C:anchored to membrane;P	O.I.	H.G.	S.X.
0.59	74.7	0.62	At4g38080	829964	hydroxyproline-rich glycoprotein family protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;PMOVBFA	O.I.	H.G.	S.X.
0.51	66.3	0.65	At2g23540	816886	GDSL-motif lipase/hydrolase family protein	F:hydrolase activity, acting on ester bonds, carboxylesterase activity;P:lipid metabolic process;C:endomembrane system;PBFOM	O.I.	H.G.	S.X.
0.47	61.2	0.61	At4g20390	827787	integral membrane family protein	F:molecular_function unknown;P:biological_process unknown;C: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
67.6 99.9 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
52.3 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
51.1 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
50.5 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
50.2 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.8 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.3 99.8 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
44.6 99.8 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.8 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.1 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
40.8 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.7 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
37.2 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
35.0 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.7 99.7 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
33.6 99.7 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
32.0 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.1 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
28.2 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.9 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
27.5 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.2 99.7 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.1 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
26.8 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.0 99.6 GSM142885 CW001_ATH1_A1.4-WestC-kub GSE6178 Mechanisms of DNA double strand break repair in Arabidopsis non-homologous end joining mutants
20.7 99.6 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.6 99.5 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
15.6 99.5 GSM133945 Murray_2-1_T0-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
14.0 99.4 GSM184497 Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
12.5 99.3 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.3 99.3 GSM133951 Murray_2-7_T12-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
11.2 99.2 GSM133950 Murray_2-6_T10-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
10.1 99.2 GSM13780 Cycloheximide GSE911 Identification of LEAFY targets during reproductive transition
9.8 99.1 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
8.9 99.0 GSM184910 Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
8.6 99.0 GSM133952 Murray_2-8_T14-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
67.6	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
52.3	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
51.1	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.5	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
50.2	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
48.8	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.3	99.8	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
44.6	99.8	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.8	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.1	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
40.8	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.7	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
37.2	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
35.0	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.7	99.7	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
33.6	99.7	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
32.0	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
31.1	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
28.2	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.9	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
27.5	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.2	99.7	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.1	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
26.8	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.0	99.6	GSM142885	CW001_ATH1_A1.4-WestC-kub	GSE6178	Mechanisms of DNA double strand break repair in Arabidopsis non-homologous end joining mutants
20.7	99.6	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
18.6	99.5	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
15.6	99.5	GSM133945	Murray_2-1_T0-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
14.0	99.4	GSM184497	Endodermis&Pericycle root cells 2hr transitory KNO3 treated, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
12.5	99.3	GSM133766	Lindsey_1-18_torpedo-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
11.3	99.3	GSM133951	Murray_2-7_T12-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
11.2	99.2	GSM133950	Murray_2-6_T10-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
10.1	99.2	GSM13780	Cycloheximide	GSE911	Identification of LEAFY targets during reproductive transition
9.8	99.1	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
8.9	99.0	GSM184910	Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
8.6	99.0	GSM133952	Murray_2-8_T14-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.095 1 GO:0010345 The chemical reactions and pathways resulting in the formation of suberin monomers and suberin polyesters. Suberin monomers are derived from fatty acids and trans-cinnamic acids. The monomers are then cross-linked with glycerols.
0.059 1 GO:0009561 The process whose specific outcome is the progression of the embryo sac over time, from its formation as the megaspore to the mature structure. The process begins when three of the four haploid megaspores disintegrate, and the fourth undergoes mitosis giving rise to a binucleate syncytial embryo sac. The two haploid nuclei migrate to the opposite poles of the embryo sac and then undergo two rounds of mitosis generating four haploid nuclei at each pole. One nucleus from each set of four migrates to the center of the cell. Cellularization occurs, resulting in an eight-nucleate seven-celled structure. This structure contains two synergid cells and an egg cell at the micropylar end, and three antipodal cells at the other end. A binucleate endosperm mother cell is formed at the center.
0.044 3 GO:0006869 The directed movement of lipids into, out of, within or between cells. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.

SF	Genes	GO ID	Process Name
0.095	1	GO:0010345	The chemical reactions and pathways resulting in the formation of suberin monomers and suberin polyesters. Suberin monomers are derived from fatty acids and trans-cinnamic acids. The monomers are then cross-linked with glycerols.
0.059	1	GO:0009561	The process whose specific outcome is the progression of the embryo sac over time, from its formation as the megaspore to the mature structure. The process begins when three of the four haploid megaspores disintegrate, and the fourth undergoes mitosis giving rise to a binucleate syncytial embryo sac. The two haploid nuclei migrate to the opposite poles of the embryo sac and then undergo two rounds of mitosis generating four haploid nuclei at each pole. One nucleus from each set of four migrates to the center of the cell. Cellularization occurs, resulting in an eight-nucleate seven-celled structure. This structure contains two synergid cells and an egg cell at the micropylar end, and three antipodal cells at the other end. A binucleate endosperm mother cell is formed at the center.
0.044	3	GO:0006869	The directed movement of lipids into, out of, within or between cells. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.021 1 00360 Phenylalanine metabolism
0.021 1 00680 Methane metabolism
0.017 1 00940 Phenylpropanoid biosynthesis

SF	Genes	KEGG ID	Pathway name
0.021	1	00360	Phenylalanine metabolism
0.021	1	00680	Methane metabolism
0.017	1	00940	Phenylpropanoid biosynthesis

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	At1g54540
Gene name	-
Module size	16 genes
NF	0.68
%ile	87.5

Co-expression analysis

Gene ID At1g54540 Gene name - Module size 16 genes NF 0.68 %ile 87.5

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 KEGG0.021100360Phenylalanine metabolism0.021100680Methane metabolism0.017100940Phenylpropanoid biosynthesis

Inter-species module comparison

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

Gene ID At1g54540

Gene name -

Module size 16 genes

NF 0.68

%ile 87.5

: 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
0.021 1 00360 Phenylalanine metabolism
0.021 1 00680 Methane metabolism
0.017 1 00940 Phenylpropanoid biosynthesis

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