CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g61000

Gene name replication protein, putative

Module size 5 genes

NF 0.84

%ile 96.0

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 At5g61000 836221 replication protein, putative F:DNA binding, nucleic acid binding;P:DNA replication;C:nucleus;PMOFA O.I. H.G. S.X.
1.00 100.0 0.95 At5g08020 830696 RPA70B (RPA70-KDA SUBUNIT B) Encodes a homolog of Replication Protein A. rpa70b mutants are hypersensitive to UV-B radiation and MMS treatments suggesting a role for this protein in DNA damage repair. O.I. H.G. S.X.
0.89 94.6 0.93 At3g24495 822040 MSH7 (MUTS HOMOLOG 7) encodes a DNA mismatch repair homolog of human MutS gene, MSH6. There are four MutS genes in Arabidopsis, MSH2, MSH3, MSH6, and MSH7, which all act as heterodimers and bind to 51-mer duplexes. MSH2MSH7 exhibit moderate affinity for a (T/G) substrate and weak binding of (+T), suggesting MSH2MSH7 may be specialized for lesions/base mispairs not tested or for (T/G) mispairs in special contexts. O.I. H.G. S.X.
0.89 94.6 0.94 At5g43080 834324 CYCA3 F:cyclin-dependent protein kinase regulator activity;P:regulation of cell cycle;C:nucleus;MPOFV O.I. H.G. S.X.
0.44 57.2 0.91 At3g18524 821383 MSH2 (MUTS HOMOLOG 2) Encodes a DNA mismatch repair homolog of human MutS gene, MSH6. MSH2 is involved in maintaining genome stability and repressing recombination of mismatched heteroduplexes.There are four MutS genes in Arabidopsis, MSH2, MSH3, MSH6, and MSH7, which all act as heterodimers and bind to 51-mer duplexes. MSH2 has different binding specificity to different mismatches in combination with MSH3, MSH6, or MSH7. 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	At5g61000	836221	replication protein, putative	F:DNA binding, nucleic acid binding;P:DNA replication;C:nucleus;PMOFA	O.I.	H.G.	S.X.
1.00	100.0	0.95	At5g08020	830696	RPA70B (RPA70-KDA SUBUNIT B)	Encodes a homolog of Replication Protein A. rpa70b mutants are hypersensitive to UV-B radiation and MMS treatments suggesting a role for this protein in DNA damage repair.	O.I.	H.G.	S.X.
0.89	94.6	0.93	At3g24495	822040	MSH7 (MUTS HOMOLOG 7)	encodes a DNA mismatch repair homolog of human MutS gene, MSH6. There are four MutS genes in Arabidopsis, MSH2, MSH3, MSH6, and MSH7, which all act as heterodimers and bind to 51-mer duplexes. MSH2MSH7 exhibit moderate affinity for a (T/G) substrate and weak binding of (+T), suggesting MSH2MSH7 may be specialized for lesions/base mispairs not tested or for (T/G) mispairs in special contexts.	O.I.	H.G.	S.X.
0.89	94.6	0.94	At5g43080	834324	CYCA3	F:cyclin-dependent protein kinase regulator activity;P:regulation of cell cycle;C:nucleus;MPOFV	O.I.	H.G.	S.X.
0.44	57.2	0.91	At3g18524	821383	MSH2 (MUTS HOMOLOG 2)	Encodes a DNA mismatch repair homolog of human MutS gene, MSH6. MSH2 is involved in maintaining genome stability and repressing recombination of mismatched heteroduplexes.There are four MutS genes in Arabidopsis, MSH2, MSH3, MSH6, and MSH7, which all act as heterodimers and bind to 51-mer duplexes. MSH2 has different binding specificity to different mismatches in combination with MSH3, MSH6, or MSH7.	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
305.2 100.0 GSM284392 Arabidopsis GCE1 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
294.2 100.0 GSM284393 Arabidopsis GCE2 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
201.6 100.0 GSM284394 Arabidopsis GCE3 GSE11262 Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
91.5 99.9 GSM131453 AtGen_6-9321_Heatstress-Roots-3.0h_Rep1 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
84.4 99.9 GSM131454 AtGen_6-9322_Heatstress-Roots-3.0h_Rep2 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
81.0 99.9 GSM311279 Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
80.4 99.9 GSM311280 Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2 GSE12402 Expression data from Arabidopsis seed compartments at the pre-globular stage
50.0 99.8 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
46.9 99.8 GSM131452 AtGen_6-9312_Heatstress-Shoots-3.0h_Rep2 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
45.1 99.8 GSM131451 AtGen_6-9311_Heatstress-Shoots-3.0h_Rep1 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
33.2 99.7 E-MEXP-98-raw-cel-320188914
29.9 99.7 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.3 99.7 GSM131448 AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
26.6 99.7 E-MEXP-98-raw-cel-320188969
26.1 99.7 GSM131449 AtGen_6-9221_Heatstress-Roots-1.0h_Rep1 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
23.3 99.6 GSM142593 DB001_ATH1_A3-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells
23.3 99.6 GSM131447 AtGen_6-9211_Heatstress-Shoots-1.0h_Rep1 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
22.9 99.6 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.2 99.6 GSM131450 AtGen_6-9222_Heatstress-Roots-1.0h_Rep2 GSE5628 AtGenExpress: Stress Treatments (Heat stress)
15.4 99.5 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.4 99.4 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.1 99.4 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.3 99.3 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.8 99.3 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.3 99.3 GSM270870 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
10.9 99.2 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.8 99.2 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.7 99.2 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.7 99.2 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.7 99.2 GSM142592 DB001_ATH1_A2-Brown-cal GSE6148 The trans-differentiation of cultured Arabidopsis cells
10.5 99.2 GSM133723 McCormac_1-1_wildtype-NFtreated_Rep1_ATH1 GSE5726 Seedling transcriptome affected by Norflurazon-induced photobleaching of chloroplasts
10.4 99.2 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.2 99.2 GSM270868 Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2 GSE10719 Response of Arabidopsis cell culture to phytoprostane A1
10.1 99.2 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.5 99.1 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.4 99.1 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.7 99.0 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
305.2	100.0	GSM284392	Arabidopsis GCE1	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
294.2	100.0	GSM284393	Arabidopsis GCE2	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
201.6	100.0	GSM284394	Arabidopsis GCE3	GSE11262	Expression data from Arabidopsis Seed Compartments at the Globular Embryo Stage.
91.5	99.9	GSM131453	AtGen_6-9321_Heatstress-Roots-3.0h_Rep1	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
84.4	99.9	GSM131454	AtGen_6-9322_Heatstress-Roots-3.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
81.0	99.9	GSM311279	Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 1	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
80.4	99.9	GSM311280	Laser capture microdissected (LCM) chalazal endosperm at the pre-globular stage, biological replicate 2	GSE12402	Expression data from Arabidopsis seed compartments at the pre-globular stage
50.0	99.8	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
46.9	99.8	GSM131452	AtGen_6-9312_Heatstress-Shoots-3.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
45.1	99.8	GSM131451	AtGen_6-9311_Heatstress-Shoots-3.0h_Rep1	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
33.2	99.7	E-MEXP-98-raw-cel-320188914
29.9	99.7	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
28.3	99.7	GSM131448	AtGen_6-9212_Heatstress-Shoots-1.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
26.6	99.7	E-MEXP-98-raw-cel-320188969
26.1	99.7	GSM131449	AtGen_6-9221_Heatstress-Roots-1.0h_Rep1	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
23.3	99.6	GSM142593	DB001_ATH1_A3-Brown-cal	GSE6148	The trans-differentiation of cultured Arabidopsis cells
23.3	99.6	GSM131447	AtGen_6-9211_Heatstress-Shoots-1.0h_Rep1	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
22.9	99.6	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
19.2	99.6	GSM131450	AtGen_6-9222_Heatstress-Roots-1.0h_Rep2	GSE5628	AtGenExpress: Stress Treatments (Heat stress)
15.4	99.5	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
13.4	99.4	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.1	99.4	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.3	99.3	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.8	99.3	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.3	99.3	GSM270870	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep3	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
10.9	99.2	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.8	99.2	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.7	99.2	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.7	99.2	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.7	99.2	GSM142592	DB001_ATH1_A2-Brown-cal	GSE6148	The trans-differentiation of cultured Arabidopsis cells
10.5	99.2	GSM133723	McCormac_1-1_wildtype-NFtreated_Rep1_ATH1	GSE5726	Seedling transcriptome affected by Norflurazon-induced photobleaching of chloroplasts
10.4	99.2	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.2	99.2	GSM270868	Arabidopsis cell culture, 4 h_response to phytoprostane A1_rep2	GSE10719	Response of Arabidopsis cell culture to phytoprostane A1
10.1	99.2	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.5	99.1	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
9.4	99.1	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
8.7	99.0	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.333 1 GO:0045128 Any process that decreases the frequency, rate or extent of recombination during meiosis. Reciprocal meiotic recombination is the cell cycle process whereby double strand breaks are formed and repaired through a double Holliday junction intermediate.
0.200 2 GO:0006298 A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
0.074 2 GO:0006260 The process whereby new strands of DNA are synthesized. The template for replication can either be an existing DNA molecule or RNA.

SF	Genes	GO ID	Process Name
0.333	1	GO:0045128	Any process that decreases the frequency, rate or extent of recombination during meiosis. Reciprocal meiotic recombination is the cell cycle process whereby double strand breaks are formed and repaired through a double Holliday junction intermediate.
0.200	2	GO:0006298	A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
0.074	2	GO:0006260	The process whereby new strands of DNA are synthesized. The template for replication can either be an existing DNA molecule or RNA.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.065 1 03430 Mismatch repair

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.065	1	03430	Mismatch 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

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Gene ID	At5g61000
Gene name	replication protein, putative
Module size	5 genes
NF	0.84
%ile	96.0

Co-expression analysis

Gene ID At5g61000 Gene name replication protein, putative Module size 5 genes NF 0.84 %ile 96.0

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 KEGG0.065103430Mismatch 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 At5g61000

Gene name replication protein, putative

Module size 5 genes

NF 0.84

%ile 96.0

: 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
0.065 1 03430 Mismatch 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