CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At2g21320

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

Module size 5 genes

NF 0.29

%ile 36.1

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
0.36 43.6 1.00 At2g21320 816671 zinc finger (B-box type) family protein F:transcription factor activity, zinc ion binding;P:regulation of transcription;C:endomembrane system, intracellular;POM O.I. H.G. S.X.
0.40 50.8 0.77 At1g32900 840184 starch synthase, putative F:transferase activity, transferring glycosyl groups;P:biosynthetic process, glucan biosynthetic process;C:chloroplast;PBOAFM O.I. H.G. S.X.
0.33 38.1 0.72 At5g24120 832477 SIGE (SIGMA FACTOR E) Encodes a specialized sigma factor that functions in regulation of plastid genes and is responsible for the light-dependent transcription at the psbD LRP. Activation of SIG5 is dependent upon blue light and mediated by cryptochromes. O.I. H.G. S.X.
0.29 30.3 0.76 At3g56290 824796 unknown protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.
0.18 11.4 0.73 At2g46830 819296 CCA1 (CIRCADIAN CLOCK ASSOCIATED 1) Encodes a transcriptional repressor that performs overlapping functions with LHY in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis. Binds to the evening element in the promoter of TOC1 and represses TOC1 transcription. CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.36	43.6	1.00	At2g21320	816671	zinc finger (B-box type) family protein	F:transcription factor activity, zinc ion binding;P:regulation of transcription;C:endomembrane system, intracellular;POM	O.I.	H.G.	S.X.
0.40	50.8	0.77	At1g32900	840184	starch synthase, putative	F:transferase activity, transferring glycosyl groups;P:biosynthetic process, glucan biosynthetic process;C:chloroplast;PBOAFM	O.I.	H.G.	S.X.
0.33	38.1	0.72	At5g24120	832477	SIGE (SIGMA FACTOR E)	Encodes a specialized sigma factor that functions in regulation of plastid genes and is responsible for the light-dependent transcription at the psbD LRP. Activation of SIG5 is dependent upon blue light and mediated by cryptochromes.	O.I.	H.G.	S.X.
0.29	30.3	0.76	At3g56290	824796	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	H.G.	S.X.
0.18	11.4	0.73	At2g46830	819296	CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)	Encodes a transcriptional repressor that performs overlapping functions with LHY in a regulatory feedback loop that is closely associated with the circadian oscillator of Arabidopsis. Binds to the evening element in the promoter of TOC1 and represses TOC1 transcription. CCA1 and LHY colocalize in the nucleus and form heterodimers in vivo. CCA1 and LHY function synergistically in regulating circadian rhythms of Arabidopsis.	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
20.6 99.6 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
15.7 99.5 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.4 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
15.2 99.4 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.7 99.4 GSM106923 opr3_OPDA_2 hrs_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.6 99.4 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5 99.4 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5 99.4 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.4 99.4 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
14.2 99.4 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.2 99.4 GSM142736 DH001_ATH1_A3-TCP1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
13.9 99.4 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.7 99.4 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.6 99.4 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.4 99.4 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.4 99.4 GSM133959 Fukuda_1-4_2B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
13.1 99.4 GSM133958 Fukuda_1-3_2A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
13.1 99.4 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
13.1 99.4 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.3 99.3 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.3 99.3 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.1 99.3 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.9 99.3 GSM106907 opr3_JA_0.5 hr_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.9 99.3 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.5 99.3 GSM142739 DH001_ATH1_A6-TCP2 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
11.4 99.3 GSM133966 Fukuda_1-11_10A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.2 99.2 GSM106825 opr3_0 hr_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.8 99.2 GSM142735 DH001_ATH1_A2-BCP1 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
10.8 99.2 GSM142738 DH001_ATH1_A5-BCP2 GSE6162 Transcriptome analysis of Arabidopsis microgametogenesis
10.5 99.2 GSM133964 Fukuda_1-9_8A_Rep1_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
10.4 99.2 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
10.2 99.2 GSM106922 opr3_OPDA_2 hrs_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.9 99.1 GSM106827 opr3_0 hr_Rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.7 99.1 GSM133967 Fukuda_1-12_10B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.6 99.1 GSM106910 opr3_JA_2 hrs_rep2 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.3 99.1 GSM106919 opr3_OPDA_0.5 hr_Rep1 GSE4733 Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.2 99.1 GSM311278 Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
9.0 99.1 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.8 99.0 GSM133965 Fukuda_1-10_8B_Rep2_ATH1 GSE5748 In vitro tracheary element transdifferentiation of Col-0 suspension cells.

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
20.6	99.6	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
15.7	99.5	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.4	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
15.2	99.4	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.7	99.4	GSM106923	opr3_OPDA_2 hrs_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
14.6	99.4	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5	99.4	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5	99.4	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.4	99.4	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
14.2	99.4	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.2	99.4	GSM142736	DH001_ATH1_A3-TCP1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
13.9	99.4	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.7	99.4	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.6	99.4	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.4	99.4	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.4	99.4	GSM133959	Fukuda_1-4_2B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
13.1	99.4	GSM133958	Fukuda_1-3_2A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
13.1	99.4	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
13.1	99.4	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.3	99.3	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.3	99.3	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.1	99.3	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.9	99.3	GSM106907	opr3_JA_0.5 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
11.9	99.3	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.5	99.3	GSM142739	DH001_ATH1_A6-TCP2	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
11.4	99.3	GSM133966	Fukuda_1-11_10A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
11.2	99.2	GSM106825	opr3_0 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
10.8	99.2	GSM142735	DH001_ATH1_A2-BCP1	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
10.8	99.2	GSM142738	DH001_ATH1_A5-BCP2	GSE6162	Transcriptome analysis of Arabidopsis microgametogenesis
10.5	99.2	GSM133964	Fukuda_1-9_8A_Rep1_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
10.4	99.2	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
10.2	99.2	GSM106922	opr3_OPDA_2 hrs_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.9	99.1	GSM106827	opr3_0 hr_Rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.7	99.1	GSM133967	Fukuda_1-12_10B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.
9.6	99.1	GSM106910	opr3_JA_2 hrs_rep2	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.3	99.1	GSM106919	opr3_OPDA_0.5 hr_Rep1	GSE4733	Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling
9.2	99.1	GSM311278	Laser capture microdissected (LCM) peripheral endosperm at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
9.0	99.1	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.8	99.0	GSM133965	Fukuda_1-10_8B_Rep2_ATH1	GSE5748	In vitro tracheary element transdifferentiation of Col-0 suspension cells.

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.333 1 GO:0010243 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic nitrogen stimulus. An organic nitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
0.286 1 GO:0009250 The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
0.200 1 GO:0048574 A change from the vegetative to the reproductive phase as a result of detection of, or exposure to, a period of light that exceeds the critical day length. The critical day length varies between species. Although the term is long-day is used, most species actually respond to the duration of the night, so that the response will occur when a period of darkness falls short of the number of hours defined by 24 minus the critical day length.

SF	Genes	GO ID	Process Name
0.333	1	GO:0010243	A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic nitrogen stimulus. An organic nitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
0.286	1	GO:0009250	The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues.
0.200	1	GO:0048574	A change from the vegetative to the reproductive phase as a result of detection of, or exposure to, a period of light that exceeds the critical day length. The critical day length varies between species. Although the term is long-day is used, most species actually respond to the duration of the night, so that the response will occur when a period of darkness falls short of the number of hours defined by 24 minus the critical day length.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.059 1 04712 Circadian rhythm - plant

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.059	1	04712	Circadian rhythm - plant

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	At2g21320
Gene name	zinc finger (B-box type) family protein
Module size	5 genes
NF	0.29
%ile	36.1

Co-expression analysis

Gene ID At2g21320 Gene name zinc finger (B-box type) family protein Module size 5 genes NF 0.29 %ile 36.1

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 KEGG0.059104712Circadian rhythm - plant

Inter-species module comparison

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

Gene ID At2g21320

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

Module size 5 genes

NF 0.29

%ile 36.1

: 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
0.059 1 04712 Circadian rhythm - plant

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