CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g05675

Gene name protein binding

Module size 7 genes

NF 0.41

%ile 57.2

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
0.53 68.6 1.00 At3g05675 819735 protein binding F:protein binding;P:unknown;C:unknown;P O.I. H.G. S.X.
0.67 81.6 0.91 At4g26980 828806 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOF O.I. H.G. S.X.
0.50 65.3 0.91 At5g15710 831425 F-box family protein F:molecular_function unknown;P:biological_process unknown;C:unknown;P O.I. H.G. S.X.
0.44 57.2 0.92 At3g07930 819984 HhH-GPD base excision DNA repair family protein F:unknown;P:base-excision repair;C:unknown;MPO O.I. H.G. S.X.
0.30 32.1 0.91 At5g65540 836680 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBV O.I. H.G. S.X.
0.29 30.3 0.91 At1g49350 841358 pfkB-type carbohydrate kinase family protein F:kinase activity, ribokinase activity;P:D-ribose metabolic process;C:cellular_component unknown;BOMFP O.I. H.G. S.X.
0.25 22.6 0.91 At5g03415 831847 DPB Encodes a homolog of the animal DP protein. DP, in animals, forms a heterodimer with E2F and plays a central role in G1/S transition in the cell division cycle. DPB has been shown to interact with non phosphorylated E2Fc; when E2Fc is phosphorylated, the formation of the E2Fc/DPB heterodimer is lost. O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.53	68.6	1.00	At3g05675	819735	protein binding	F:protein binding;P:unknown;C:unknown;P	O.I.	H.G.	S.X.
0.67	81.6	0.91	At4g26980	828806	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MPOF	O.I.	H.G.	S.X.
0.50	65.3	0.91	At5g15710	831425	F-box family protein	F:molecular_function unknown;P:biological_process unknown;C:unknown;P	O.I.	H.G.	S.X.
0.44	57.2	0.92	At3g07930	819984	HhH-GPD base excision DNA repair family protein	F:unknown;P:base-excision repair;C:unknown;MPO	O.I.	H.G.	S.X.
0.30	32.1	0.91	At5g65540	836680	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;OMPFBV	O.I.	H.G.	S.X.
0.29	30.3	0.91	At1g49350	841358	pfkB-type carbohydrate kinase family protein	F:kinase activity, ribokinase activity;P:D-ribose metabolic process;C:cellular_component unknown;BOMFP	O.I.	H.G.	S.X.
0.25	22.6	0.91	At5g03415	831847	DPB	Encodes a homolog of the animal DP protein. DP, in animals, forms a heterodimer with E2F and plays a central role in G1/S transition in the cell division cycle. DPB has been shown to interact with non phosphorylated E2Fc; when E2Fc is phosphorylated, the formation of the E2Fc/DPB heterodimer is lost.	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
75.5 99.9 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.0 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
64.7 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.3 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.6 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.4 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.5 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.9 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6 99.8 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.1 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.5 99.8 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
45.9 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.2 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.5 99.8 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.0 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
38.4 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.7 99.7 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
32.4 99.7 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
30.4 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
22.2 99.6 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
21.1 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
19.6 99.6 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.7 99.5 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
16.9 99.5 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.1 99.4 GSM176876 AWP_AL_Txed_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
13.1 99.4 GSM133719 Deeken_A-1-Deeke-Tum_SLD_REP1 GSE5725 Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana
12.6 99.3 E-MEXP-1607-raw-cel-1620685818
11.0 99.2 GSM131329 AtGen_6-3621_Saltstress-Roots-24.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
11.0 99.2 GSM131325 AtGen_6-3521_Saltstress-Roots-12.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
11.0 99.2 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.0 99.2 GSM131321 AtGen_6-3421_Saltstress-Roots-6.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
10.9 99.2 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.6 99.2 GSM131322 AtGen_6-3422_Saltstress-Roots-6.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
10.3 99.2 GSM131317 AtGen_6-3321_Saltstress-Roots-3.0h_Rep1 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
9.8 99.1 GSM131318 AtGen_6-3322_Saltstress-Roots-3.0h_Rep2 GSE5623 AtGenExpress: Stress Treatments (Salt stress)
9.8 99.1 GSM176879 AWP_Control_1 GSE7334 Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.7 99.1 GSM75508 Col-0 0h NAA replicate 1 GSE3350 SLR/IAA14-dependent auxin induced lateral root initiation
9.7 99.1 GSM131290 AtGen_6-2222_Osmoticstress-Roots-1.0h_Rep2 GSE5622 AtGenExpress: Stress Treatments (Osmotic stress)
9.0 99.1 GSM239251 Columbia glabrous (C24) wild type pollen GSE9408 Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
9.0 99.1 GSM142592 DB001_ATH1_A2-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
75.5	99.9	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
69.0	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
64.7	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.3	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.6	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
57.4	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.5	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.9	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6	99.8	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.1	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.5	99.8	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
45.9	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
43.2	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.5	99.8	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
41.0	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
38.4	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.7	99.7	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
32.4	99.7	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
30.4	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
22.2	99.6	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
21.1	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
19.6	99.6	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
18.7	99.5	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
16.9	99.5	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.1	99.4	GSM176876	AWP_AL_Txed_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
13.1	99.4	GSM133719	Deeken_A-1-Deeke-Tum_SLD_REP1	GSE5725	Agrobacterium tumefaciens-induced tumour development of Arabidopsis thaliana
12.6	99.3	E-MEXP-1607-raw-cel-1620685818
11.0	99.2	GSM131329	AtGen_6-3621_Saltstress-Roots-24.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
11.0	99.2	GSM131325	AtGen_6-3521_Saltstress-Roots-12.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
11.0	99.2	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.0	99.2	GSM131321	AtGen_6-3421_Saltstress-Roots-6.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
10.9	99.2	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
10.6	99.2	GSM131322	AtGen_6-3422_Saltstress-Roots-6.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
10.3	99.2	GSM131317	AtGen_6-3321_Saltstress-Roots-3.0h_Rep1	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
9.8	99.1	GSM131318	AtGen_6-3322_Saltstress-Roots-3.0h_Rep2	GSE5623	AtGenExpress: Stress Treatments (Salt stress)
9.8	99.1	GSM176879	AWP_Control_1	GSE7334	Microarray Analysis of Arabidopsis Genome Response to Aluminum Stress
9.7	99.1	GSM75508	Col-0 0h NAA replicate 1	GSE3350	SLR/IAA14-dependent auxin induced lateral root initiation
9.7	99.1	GSM131290	AtGen_6-2222_Osmoticstress-Roots-1.0h_Rep2	GSE5622	AtGenExpress: Stress Treatments (Osmotic stress)
9.0	99.1	GSM239251	Columbia glabrous (C24) wild type pollen	GSE9408	Identification of putative Arabidopsis DEMETER target genes by GeneChip Analysis
9.0	99.1	GSM142592	DB001_ATH1_A2-Brown-cal	GSE6148	The trans-differentiation of cultured Arabidopsis cells

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.182 1 GO:0000082 Progression from G1 phase to S phase of the mitotic cell cycle.
0.118 1 GO:0006014 The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose moiety of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
0.077 1 GO:0042023 Regulated re-replication of DNA within a single cell cycle, resulting in an increased cell ploidy. For example, occurs in the synthesis of Drosophila salivary gland cell polytene chromosomes.

SF	Genes	GO ID	Process Name
0.182	1	GO:0000082	Progression from G1 phase to S phase of the mitotic cell cycle.
0.118	1	GO:0006014	The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose moiety of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
0.077	1	GO:0042023	Regulated re-replication of DNA within a single cell cycle, resulting in an increased cell ploidy. For example, occurs in the synthesis of Drosophila salivary gland cell polytene chromosomes.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.044 1 03410 Base excision repair

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.044	1	03410	Base excision repair

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	At3g05675
Gene name	protein binding
Module size	7 genes
NF	0.41
%ile	57.2

Co-expression analysis

Gene ID At3g05675 Gene name protein binding Module size 7 genes NF 0.41 %ile 57.2

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 KEGG0.044103410Base excision repair

Inter-species module comparison

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

Gene ID At3g05675

Gene name protein binding

Module size 7 genes

NF 0.41

%ile 57.2

: 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
0.044 1 03410 Base excision repair

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