CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At4g39070

Gene name zinc finger (B-box type) family protein

Module size 6 genes

NF 0.07

%ile 4.3

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 At4g39070 830062 zinc finger (B-box type) family protein F:transcription factor activity, zinc ion binding;P:response to chitin, regulation of transcription;C:intracellular;POM O.I. H.G. S.X.
0.29 30.3 0.76 At1g18270 838407 ketose-bisphosphate aldolase class-II family protein F:in 8 functions;P:pentose-phosphate shunt, valine metabolic process, glycolysis, metabolic process;C:nucleus;BOFMPA O.I. H.G. S.X.
0.25 22.6 0.79 At5g28050 832875 cytidine/deoxycytidylate deaminase family protein F:hydrolase activity, zinc ion binding, catalytic activity;P:pyrimidine ribonucleotide metabolic process, pyrimidine deoxyribonucleoside interconversion, deoxyribose phosphate metabolic process, anaerobic respiration;C:cellular_component unknown;BOFMPA O.I. H.G. S.X.
0.20 14.4 0.77 At2g14170 815903 ALDH6B2 Arabidopsis thaliana methylmalonate-semialdehyde dehydrogenase O.I. H.G. S.X.
0.13 5.8 0.76 At5g26740 832714 unknown protein F:unknown;P:unknown;C:endomembrane system;MPFO O.I. H.G. S.X.
0.01 0.2 0.76 At1g30130 839892 unknown protein F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;OBPF 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	At4g39070	830062	zinc finger (B-box type) family protein	F:transcription factor activity, zinc ion binding;P:response to chitin, regulation of transcription;C:intracellular;POM	O.I.	H.G.	S.X.
0.29	30.3	0.76	At1g18270	838407	ketose-bisphosphate aldolase class-II family protein	F:in 8 functions;P:pentose-phosphate shunt, valine metabolic process, glycolysis, metabolic process;C:nucleus;BOFMPA	O.I.	H.G.	S.X.
0.25	22.6	0.79	At5g28050	832875	cytidine/deoxycytidylate deaminase family protein	F:hydrolase activity, zinc ion binding, catalytic activity;P:pyrimidine ribonucleotide metabolic process, pyrimidine deoxyribonucleoside interconversion, deoxyribose phosphate metabolic process, anaerobic respiration;C:cellular_component unknown;BOFMPA	O.I.	H.G.	S.X.
0.20	14.4	0.77	At2g14170	815903	ALDH6B2	Arabidopsis thaliana methylmalonate-semialdehyde dehydrogenase	O.I.	H.G.	S.X.
0.13	5.8	0.76	At5g26740	832714	unknown protein	F:unknown;P:unknown;C:endomembrane system;MPFO	O.I.	H.G.	S.X.
0.01	0.2	0.76	At1g30130	839892	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:endomembrane system;OBPF	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
61.8 99.8 E-ATMX-35-raw-cel-1574334832
54.0 99.8 E-ATMX-35-raw-cel-1574334816
20.9 99.6 E-ATMX-35-raw-cel-1574334800
19.6 99.6 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
19.6 99.6 GSM131279 AtGen_6-1611_Cold(4°C)-Shoots-24.0h_Rep1 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
17.7 99.5 GSM184913 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt
15.1 99.4 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
15.0 99.4 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
14.9 99.4 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.5 99.3 GSM74900 Wildtype_24H Cold_Rep1 GSE3326 ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
11.0 99.2 GSM74901 Wildtype_24H Cold_Rep2 GSE3326 ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
10.9 99.2 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.7 99.2 GSM131276 AtGen_6-1512_Cold(4°C)-Shoots-12.0h_Rep2 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
10.6 99.2 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.5 99.2 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
10.3 99.2 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.2 99.2 GSM131281 AtGen_6-1621_Cold(4°C)-Roots-24.0h_Rep1 GSE5621 AtGenExpress: Stress Treatments (Cold stress)
10.2 99.2 GSM133407 Bramke_A1-warre-WTC GSE5711 Cold induced changes: differences between the Arabidopsis thaliana wild type and freezing sensitive mutants.
10.1 99.2 GSM184914 Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
9.9 99.1 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8 99.1 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7 99.1 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7 99.1 GSM133773 Lindsey_1-25_torpedo-meristem_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.4 99.1 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.2 99.1 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.1 99.1 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
8.9 99.0 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8 99.0 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8 99.0 GSM131282 AtGen_6-1622_Cold(4°C)-Roots-24.0h_Rep2 GSE5621 AtGenExpress: Stress Treatments (Cold stress)

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
61.8	99.8	E-ATMX-35-raw-cel-1574334832
54.0	99.8	E-ATMX-35-raw-cel-1574334816
20.9	99.6	E-ATMX-35-raw-cel-1574334800
19.6	99.6	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
19.6	99.6	GSM131279	AtGen_6-1611_Cold(4°C)-Shoots-24.0h_Rep1	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
17.7	99.5	GSM184913	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt
15.1	99.4	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
15.0	99.4	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
14.9	99.4	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.5	99.3	GSM74900	Wildtype_24H Cold_Rep1	GSE3326	ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
11.0	99.2	GSM74901	Wildtype_24H Cold_Rep2	GSE3326	ICE1 regulation of the Arabidopsis Cold-Responsive Transcriptome
10.9	99.2	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.7	99.2	GSM131276	AtGen_6-1512_Cold(4°C)-Shoots-12.0h_Rep2	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
10.6	99.2	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.5	99.2	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
10.3	99.2	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.2	99.2	GSM131281	AtGen_6-1621_Cold(4°C)-Roots-24.0h_Rep1	GSE5621	AtGenExpress: Stress Treatments (Cold stress)
10.2	99.2	GSM133407	Bramke_A1-warre-WTC	GSE5711	Cold induced changes: differences between the Arabidopsis thaliana wild type and freezing sensitive mutants.
10.1	99.2	GSM184914	Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
9.9	99.1	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.8	99.1	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7	99.1	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.7	99.1	GSM133773	Lindsey_1-25_torpedo-meristem_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.4	99.1	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4	99.1	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.2	99.1	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.1	99.1	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
8.9	99.0	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8	99.0	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
8.8	99.0	GSM131282	AtGen_6-1622_Cold(4°C)-Roots-24.0h_Rep2	GSE5621	AtGenExpress: Stress Treatments (Cold stress)

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.250 1 GO:0006573 The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid.
0.087 1 GO:0006098 The process by which glucose is oxidized, coupled to NADPH synthesis. Glucose 6-P is oxidized with the formation of carbon dioxide (CO2), ribulose 5-phosphate and reduced NADP; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
0.038 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
0.250	1	GO:0006573	The chemical reactions and pathways involving valine, 2-amino-3-methylbutanoic acid.
0.087	1	GO:0006098	The process by which glucose is oxidized, coupled to NADPH synthesis. Glucose 6-P is oxidized with the formation of carbon dioxide (CO2), ribulose 5-phosphate and reduced NADP; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
0.038	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
0.080 1 00640 Propanoate metabolism
0.049 1 00280 Valine, leucine and isoleucine degradation
0.047 1 00562 Inositol phosphate metabolism

SF	Genes	KEGG ID	Pathway name
0.080	1	00640	Propanoate metabolism
0.049	1	00280	Valine, leucine and isoleucine degradation
0.047	1	00562	Inositol phosphate 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

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Gene ID	At4g39070
Gene name	zinc finger (B-box type) family protein
Module size	6 genes
NF	0.07
%ile	4.3

Co-expression analysis

Gene ID At4g39070 Gene name zinc finger (B-box type) family protein Module size 6 genes NF 0.07 %ile 4.3

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 KEGG0.080100640Propanoate metabolism0.049100280Valine, leucine and isoleucine degradation0.047100562Inositol phosphate 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 At4g39070

Gene name zinc finger (B-box type) family protein

Module size 6 genes

NF 0.07

%ile 4.3

: 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
0.080 1 00640 Propanoate metabolism
0.049 1 00280 Valine, leucine and isoleucine degradation
0.047 1 00562 Inositol phosphate 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