CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g73870

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

Module size 5 genes

NF 0.18

%ile 15.8

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
0.40 50.8 1.00 At1g73870 843723 zinc finger (B-box type) family protein F:transcription factor activity, zinc ion binding;P:regulation of transcription;C:intracellular;PO O.I. H.G. S.X.
0.67 81.6 0.80 At1g55960 842047 - F:molecular_function unknown;P:biological_process unknown;C:unknown;MPO O.I. H.G. S.X.
0.67 81.6 0.75 At2g15020 815991 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.18 11.4 0.74 At1g64500 842758 glutaredoxin family protein F:electron carrier activity, protein disulfide oxidoreductase activity;P:N-terminal protein myristoylation, cell redox homeostasis;C:cellular_component unknown;PMBOF O.I. H.G. S.X.
0.07 1.9 0.72 At5g52570 835334 BETA-OHASE 2 (BETA-CAROTENE HYDROXYLASE 2) Converts β-carotene to zeaxanthin via cryptoxanthin. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.40	50.8	1.00	At1g73870	843723	zinc finger (B-box type) family protein	F:transcription factor activity, zinc ion binding;P:regulation of transcription;C:intracellular;PO	O.I.	H.G.	S.X.
0.67	81.6	0.80	At1g55960	842047	-	F:molecular_function unknown;P:biological_process unknown;C:unknown;MPO	O.I.	H.G.	S.X.
0.67	81.6	0.75	At2g15020	815991	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.18	11.4	0.74	At1g64500	842758	glutaredoxin family protein	F:electron carrier activity, protein disulfide oxidoreductase activity;P:N-terminal protein myristoylation, cell redox homeostasis;C:cellular_component unknown;PMBOF	O.I.	H.G.	S.X.
0.07	1.9	0.72	At5g52570	835334	BETA-OHASE 2 (BETA-CAROTENE HYDROXYLASE 2)	Converts β-carotene to zeaxanthin via cryptoxanthin.	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
134.4 99.9 GSM311282 Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
118.1 99.9 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
117.8 99.9 GSM311281 Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
116.2 99.9 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
96.5 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
96.4 99.9 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
96.3 99.9 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
87.3 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
83.3 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
77.6 99.9 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
76.2 99.9 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.8 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.0 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.6 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.2 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.0 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
44.8 99.8 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
42.8 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.3 99.8 GSM311293 Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
39.3 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.7 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.3 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.9 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.7 99.7 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.6 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.5 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
22.8 99.6 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.7 99.6 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
16.6 99.5 GSM311286 Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
16.1 99.5 GSM106916 opr3_JA_22 hrs_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
15.9 99.5 GSM142755 MJ001_ATH1_A6-jones-RH-Rep3 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
15.3 99.4 GSM311285 Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
15.0 99.4 GSM142752 MJ001_ATH1_A3-jones-rh1 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
14.2 99.4 GSM311294 Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2 GSE12403 Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
12.5 99.3 GSM184477 Lateral Root Cap root cells 2hr KCl control treated, biological rep2 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
11.6 99.3 GSM106917 opr3_JA_22 hrs_Rep3 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.4 99.3 GSM284395 Arabidopsis GPSc1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.1 99.2 GSM142753 MJ001_ATH1_A4-jones-rh2 GSE6165 The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
10.5 99.2 GSM106915 opr3_JA_22 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.4 99.2 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
10.1 99.2 GSM184511 Pericycle root cells 2hr continuous KNO3 treated, biological rep3 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
8.8 99.0 GSM157323 Hammond_3-16_Control-root_Rep3_ATH1 GSE6825 Differential gene expression patterns in potassium-starved and Caesium-treated plants

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
134.4	99.9	GSM311282	Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
118.1	99.9	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
117.8	99.9	GSM311281	Laser capture microdissected (LCM) chalazal seed coat at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
116.2	99.9	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
96.5	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
96.4	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
96.3	99.9	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
87.3	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
83.3	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
77.6	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
76.2	99.9	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
63.8	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.0	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.6	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.2	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
45.0	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
44.8	99.8	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
42.8	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.3	99.8	GSM311293	Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 1	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
39.3	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
37.7	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.3	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.9	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.7	99.7	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.6	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.5	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
22.8	99.6	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.7	99.6	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
16.6	99.5	GSM311286	Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
16.1	99.5	GSM106916	opr3_JA_22 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
15.9	99.5	GSM142755	MJ001_ATH1_A6-jones-RH-Rep3	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
15.3	99.4	GSM311285	Laser capture microdissected (LCM) whole seed sections at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
15.0	99.4	GSM142752	MJ001_ATH1_A3-jones-rh1	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
14.2	99.4	GSM311294	Laser capture microdissected (LCM) chalazal seed coat at the linear-cotyledon stage, biological replicate 2	GSE12403	Expression data from Arabidopsis seed compartments at the linear-cotyledon stage
12.5	99.3	GSM184477	Lateral Root Cap root cells 2hr KCl control treated, biological rep2	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
11.6	99.3	GSM106917	opr3_JA_22 hrs_Rep3	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.4	99.3	GSM284395	Arabidopsis GPSc1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
11.1	99.2	GSM142753	MJ001_ATH1_A4-jones-rh2	GSE6165	The effect of mutations in AtrbohC on the pattern of gene expression in primary root tissue.
10.5	99.2	GSM106915	opr3_JA_22 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.4	99.2	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
10.1	99.2	GSM184511	Pericycle root cells 2hr continuous KNO3 treated, biological rep3	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
8.8	99.0	GSM157323	Hammond_3-16_Control-root_Rep3_ATH1	GSE6825	Differential gene expression patterns in potassium-starved and Caesium-treated plants

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.286 1 GO:0016119 The chemical reactions and pathways involving carotenes, hydrocarbon carotenoids.
0.182 1 GO:0016123 The chemical reactions and pathways resulting in the formation of xanthophylls, oxygen-containing carotenoids.
0.019 1 GO:0045454 Any process that maintains the redox environment of a cell or compartment within a cell.

SF	Genes	GO ID	Process Name
0.286	1	GO:0016119	The chemical reactions and pathways involving carotenes, hydrocarbon carotenoids.
0.182	1	GO:0016123	The chemical reactions and pathways resulting in the formation of xanthophylls, oxygen-containing carotenoids.
0.019	1	GO:0045454	Any process that maintains the redox environment of a cell or compartment within a cell.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.074 1 00906 Carotenoid biosynthesis
0.010 1 01062 Biosynthesis of terpenoids and steroids
0.006 1 01070 Biosynthesis of plant hormones

SF	Genes	KEGG ID	Pathway name
0.074	1	00906	Carotenoid biosynthesis
0.010	1	01062	Biosynthesis of terpenoids and steroids
0.006	1	01070	Biosynthesis of plant hormones

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	At1g73870
Gene name	zinc finger (B-box type) family protein
Module size	5 genes
NF	0.18
%ile	15.8

Co-expression analysis

Gene ID At1g73870 Gene name zinc finger (B-box type) family protein Module size 5 genes NF 0.18 %ile 15.8

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 KEGG0.074100906Carotenoid biosynthesis0.010101062Biosynthesis of terpenoids and steroids0.006101070Biosynthesis of plant hormones

Inter-species module comparison

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

Gene ID At1g73870

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

Module size 5 genes

NF 0.18

%ile 15.8

: 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
0.074 1 00906 Carotenoid biosynthesis
0.010 1 01062 Biosynthesis of terpenoids and steroids
0.006 1 01070 Biosynthesis of plant hormones

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