CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g24580

Gene name copper-binding family protein

Module size 9 genes

NF 0.58

%ile 79.7

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 At5g24580 832529 copper-binding family protein F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:cellular_component unknown;MOPBFVA O.I. H.G. S.X.
0.74 86.1 0.68 At5g47920 834843 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO O.I. H.G. S.X.
0.71 84.2 0.64 At5g17980 831665 C2 domain-containing protein F:unknown;P:unknown;C:endoplasmic reticulum, plasma membrane;MOBFPVA O.I. H.G. S.X.
0.67 81.6 0.72 At5g24800 832549 BZIP9 (BASIC LEUCINE ZIPPER 9) Encodes bZIP protein BZO2H2. O.I. H.G. S.X.
0.63 78.1 0.65 At3g21420 821696 oxidoreductase, 2OG-Fe(II) oxygenase family protein F:oxidoreductase activity;P:metabolic process;C:cellular_component unknown;POBFM O.I. H.G. S.X.
0.59 74.7 0.73 At4g16790 827385 hydroxyproline-rich glycoprotein family protein F:unknown;P:unknown;C:unknown;MPFOBVA O.I. H.G. S.X.
0.56 73.0 0.67 At1g73850 843721 structural constituent of ribosome F:structural constituent of ribosome;P:translation;C:ribosome, intracellular;OMFPBV O.I. H.G. S.X.
0.46 59.8 0.62 At1g26450 839186 beta-1,3-glucanase-related F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;OMFPBVA O.I. H.G. S.X.
0.45 58.3 0.83 At1g77660 844102 MORN (Membrane Occupation and Recognition Nexus) repeat-containing protein /phosphatidylinositol-4-phosphate 5-kinase-related F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBPF 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	At5g24580	832529	copper-binding family protein	F:copper ion binding, metal ion binding;P:copper ion transport, metal ion transport;C:cellular_component unknown;MOPBFVA	O.I.	H.G.	S.X.
0.74	86.1	0.68	At5g47920	834843	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;PO	O.I.	H.G.	S.X.
0.71	84.2	0.64	At5g17980	831665	C2 domain-containing protein	F:unknown;P:unknown;C:endoplasmic reticulum, plasma membrane;MOBFPVA	O.I.	H.G.	S.X.
0.67	81.6	0.72	At5g24800	832549	BZIP9 (BASIC LEUCINE ZIPPER 9)	Encodes bZIP protein BZO2H2.	O.I.	H.G.	S.X.
0.63	78.1	0.65	At3g21420	821696	oxidoreductase, 2OG-Fe(II) oxygenase family protein	F:oxidoreductase activity;P:metabolic process;C:cellular_component unknown;POBFM	O.I.	H.G.	S.X.
0.59	74.7	0.73	At4g16790	827385	hydroxyproline-rich glycoprotein family protein	F:unknown;P:unknown;C:unknown;MPFOBVA	O.I.	H.G.	S.X.
0.56	73.0	0.67	At1g73850	843721	structural constituent of ribosome	F:structural constituent of ribosome;P:translation;C:ribosome, intracellular;OMFPBV	O.I.	H.G.	S.X.
0.46	59.8	0.62	At1g26450	839186	beta-1,3-glucanase-related	F:molecular_function unknown;P:biological_process unknown;C:anchored to membrane;OMFPBVA	O.I.	H.G.	S.X.
0.45	58.3	0.83	At1g77660	844102	MORN (Membrane Occupation and Recognition Nexus) repeat-containing protein /phosphatidylinositol-4-phosphate 5-kinase-related	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMBPF	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
44.7 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.2 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
39.2 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
36.3 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.8 99.7 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.1 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.7 99.7 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.0 99.7 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.4 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.9 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.4 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.6 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.0 99.7 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.6 99.7 E-MEXP-432-raw-cel-590864435
27.0 99.7 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.9 99.6 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.3 99.6 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
23.4 99.6 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
22.4 99.6 E-MEXP-432-raw-cel-590864422
21.6 99.6 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
20.4 99.6 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.3 99.5 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.0 99.5 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.8 99.5 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.2 99.5 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.1 99.5 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.5 99.5 E-MEXP-1443-raw-cel-1581869745
15.8 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
15.0 99.4 GSM142625 MC002_ATH1_A1.3-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.3 99.3 E-MEXP-1443-raw-cel-1581869803
12.0 99.3 GSM142623 MC002_ATH1_A1.1-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.9 99.3 GSM142624 MC002_ATH1_A1.2-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.4 99.3 GSM142661 MB002_ATH1_A1-Eland-ch1 GSE6153 Identification of genes involved in secondary cell wall development in the hypocotyls of short day grown Arabidopsis
11.3 99.3 GSM204026 protoplast_control_rep1 GSE8248 Identification of hypoxia-inducible genes in Arabidopsis mesophyll cells
10.9 99.2 GSM142631 MC002_ATH1_A3.3-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.9 99.2 GSM142627 MC002_ATH1_A2.2-dubos-wtc GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.8 99.2 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.4 99.2 GSM142629 MC002_ATH1_A3.1-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.1 99.2 GSM142630 MC002_ATH1_A3.2-dubos-6kx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.8 99.1 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
9.5 99.1 GSM142626 MC002_ATH1_A2.1-dubos-wtc GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.2 99.1 E-MEXP-1474-raw-cel-1593932513
9.1 99.1 GSM131656 ATGE_27_B GSE5633 AtGenExpress: Developmental series (shoots and stems)
9.1 99.1 GSM142628 MC002_ATH1_A2.3-dubos-wtc GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.1 99.1 GSM242957 Mock day 3 (day3E1) GSE9605 Target genes of AGAMOUS during early flower development in Arabidopsis
9.0 99.1 GSM142662 MB002_ATH1_A2-Eland-ch2 GSE6153 Identification of genes involved in secondary cell wall development in the hypocotyls of short day grown Arabidopsis
9.0 99.1 GSM242962 Mock day 7 (day7E2) GSE9605 Target genes of AGAMOUS during early flower development in Arabidopsis
9.0 99.1 GSM131655 ATGE_27_A GSE5633 AtGenExpress: Developmental series (shoots and stems)
8.7 99.0 GSM142634 MC002_ATH1_A4.3-dubos-6kc GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
44.7	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.2	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
39.2	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
36.3	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.8	99.7	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
35.1	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.7	99.7	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.0	99.7	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
33.4	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.9	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.4	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.6	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
30.0	99.7	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
27.6	99.7	E-MEXP-432-raw-cel-590864435
27.0	99.7	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.9	99.6	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
24.3	99.6	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
23.4	99.6	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.4	99.6	E-MEXP-432-raw-cel-590864422
21.6	99.6	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
20.4	99.6	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.3	99.5	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.0	99.5	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.8	99.5	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.2	99.5	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
17.1	99.5	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.5	99.5	E-MEXP-1443-raw-cel-1581869745
15.8	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
15.0	99.4	GSM142625	MC002_ATH1_A1.3-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
12.3	99.3	E-MEXP-1443-raw-cel-1581869803
12.0	99.3	GSM142623	MC002_ATH1_A1.1-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.9	99.3	GSM142624	MC002_ATH1_A1.2-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
11.4	99.3	GSM142661	MB002_ATH1_A1-Eland-ch1	GSE6153	Identification of genes involved in secondary cell wall development in the hypocotyls of short day grown Arabidopsis
11.3	99.3	GSM204026	protoplast_control_rep1	GSE8248	Identification of hypoxia-inducible genes in Arabidopsis mesophyll cells
10.9	99.2	GSM142631	MC002_ATH1_A3.3-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.9	99.2	GSM142627	MC002_ATH1_A2.2-dubos-wtc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.8	99.2	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.4	99.2	GSM142629	MC002_ATH1_A3.1-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
10.1	99.2	GSM142630	MC002_ATH1_A3.2-dubos-6kx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.8	99.1	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
9.5	99.1	GSM142626	MC002_ATH1_A2.1-dubos-wtc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.2	99.1	E-MEXP-1474-raw-cel-1593932513
9.1	99.1	GSM131656	ATGE_27_B	GSE5633	AtGenExpress: Developmental series (shoots and stems)
9.1	99.1	GSM142628	MC002_ATH1_A2.3-dubos-wtc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.1	99.1	GSM242957	Mock day 3 (day3E1)	GSE9605	Target genes of AGAMOUS during early flower development in Arabidopsis
9.0	99.1	GSM142662	MB002_ATH1_A2-Eland-ch2	GSE6153	Identification of genes involved in secondary cell wall development in the hypocotyls of short day grown Arabidopsis
9.0	99.1	GSM242962	Mock day 7 (day7E2)	GSE9605	Target genes of AGAMOUS during early flower development in Arabidopsis
9.0	99.1	GSM131655	ATGE_27_A	GSE5633	AtGenExpress: Developmental series (shoots and stems)
8.7	99.0	GSM142634	MC002_ATH1_A4.3-dubos-6kc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.071 1 GO:0006825 The directed movement of copper (Cu) ions into, out of, within or between cells.
0.020 1 GO:0030001 The directed movement of metal ions, any metal ion with an electric charge, into, out of, within or between cells.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.071	1	GO:0006825	The directed movement of copper (Cu) ions into, out of, within or between cells.
0.020	1	GO:0030001	The directed movement of metal ions, any metal ion with an electric charge, into, out of, within or between cells.

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	At5g24580
Gene name	copper-binding family protein
Module size	9 genes
NF	0.58
%ile	79.7

Co-expression analysis

Gene ID At5g24580 Gene name copper-binding family protein Module size 9 genes NF 0.58 %ile 79.7

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

SFGenesGO IDProcess NameLink to AmiGO0.0711GO:0006825The directed movement of copper (Cu) ions into, out of, within or between cells.0.0201GO:0030001The directed movement of metal ions, any metal ion with an electric charge, into, out of, within or between cells.

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 At5g24580

Gene name copper-binding family protein

Module size 9 genes

NF 0.58

%ile 79.7

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes GO ID Process Name Link to AmiGO
0.071 1 GO:0006825 The directed movement of copper (Cu) ions into, out of, within or between cells.
0.020 1 GO:0030001 The directed movement of metal ions, any metal ion with an electric charge, into, out of, within or between cells.

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