CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g57660

Gene name NRPA1

Module size 5 genes

NF 0.71

%ile 89.8

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
0.57 73.8 1.00 At3g57660 824935 NRPA1 Encodes a subunit of RNA polymerase I (aka RNA polymerase A). O.I. H.G. S.X.
0.89 94.6 0.95 At1g63810 842684 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPA O.I. H.G. S.X.
0.86 93.1 0.94 At1g69070 843239 - F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MBOFPVA O.I. H.G. S.X.
0.67 81.6 0.94 At2g17250 816230 EMB2762 (EMBRYO DEFECTIVE 2762) F:molecular_function unknown;P:biological_process unknown;C:membrane;FMOP O.I. H.G. S.X.
0.67 81.6 0.94 At5g11240 830994 transducin family protein / WD-40 repeat family protein F:nucleotide binding;P:biological_process unknown;C:endomembrane system;BMFOPA O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.57	73.8	1.00	At3g57660	824935	NRPA1	Encodes a subunit of RNA polymerase I (aka RNA polymerase A).	O.I.	H.G.	S.X.
0.89	94.6	0.95	At1g63810	842684	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MFOPA	O.I.	H.G.	S.X.
0.86	93.1	0.94	At1g69070	843239	-	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;MBOFPVA	O.I.	H.G.	S.X.
0.67	81.6	0.94	At2g17250	816230	EMB2762 (EMBRYO DEFECTIVE 2762)	F:molecular_function unknown;P:biological_process unknown;C:membrane;FMOP	O.I.	H.G.	S.X.
0.67	81.6	0.94	At5g11240	830994	transducin family protein / WD-40 repeat family protein	F:nucleotide binding;P:biological_process unknown;C:endomembrane system;BMFOPA	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
140.5 99.9 GSM133304 RIKEN-NAKABAYASHI1B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
135.0 99.9 GSM133303 RIKEN-NAKABAYASHI1A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
108.0 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
85.7 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
81.4 99.9 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
79.5 99.9 GSM10456 WT Post-Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
79.3 99.9 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
65.2 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
62.9 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
61.6 99.8 GSM10454 WT Post-Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
60.2 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.9 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.9 99.8 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
43.0 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.9 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
39.9 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.5 99.8 GSM10451 WT Mature Green Seed 1 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
38.3 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.3 99.8 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
35.4 99.7 GSM131702 ATGE_82_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
34.3 99.7 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.8 99.7 GSM131701 ATGE_82_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
31.8 99.7 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
31.4 99.7 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.1 99.7 GSM153927 ahg1-1 rep2 GSE6638 Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
26.9 99.7 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.1 99.6 GSM131700 ATGE_82_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
24.3 99.6 GSM133309 RIKEN-NAKABAYASHI4B GSE5700 AtGenExpress: Effect of ABA during seed imbibition
20.2 99.6 GSM153928 ahg3-1 rep1 GSE6638 Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
20.0 99.6 GSM153929 ahg3-1 rep2 GSE6638 Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
19.2 99.6 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.7 99.5 GSM153926 ahg1-1 rep1 GSE6638 Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
18.2 99.5 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
18.2 99.5 GSM133117 RIKEN-YAMAUCHI1A GSE5687 AtGenExpress: Different temperature treatment of seeds
16.4 99.5 GSM131706 ATGE_84_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
16.3 99.5 GSM131698 ATGE_81_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
15.4 99.5 GSM131699 ATGE_81_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
15.0 99.4 GSM131697 ATGE_81_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
14.4 99.4 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.2 99.4 GSM131705 ATGE_83_C GSE5634 AtGenExpress: Developmental series (siliques and seeds)
14.1 99.4 GSM131707 ATGE_84_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
13.9 99.4 GSM131708 ATGE_84_D GSE5634 AtGenExpress: Developmental series (siliques and seeds)
13.5 99.4 GSM131703 ATGE_83_A GSE5634 AtGenExpress: Developmental series (siliques and seeds)
12.6 99.3 E-MEXP-509-raw-cel-829148561
12.5 99.3 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
10.7 99.2 E-MEXP-1443-raw-cel-1581869573
10.0 99.2 GSM133308 RIKEN-NAKABAYASHI4A GSE5700 AtGenExpress: Effect of ABA during seed imbibition
10.0 99.2 GSM153925 ABA control rep2 GSE6638 Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
9.9 99.1 GSM131704 ATGE_83_B GSE5634 AtGenExpress: Developmental series (siliques and seeds)
9.7 99.1 GSM10453 WT Mature Green Seed 2 GSE680 Transcript Profiling of Arabidopsis Plant Life Cycle
9.6 99.1 GSM142625 MC002_ATH1_A1.3-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.5 99.1 GSM142642 MC002_ATH1_A7.2-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.5 99.1 GSM142643 MC002_ATH1_A7.3-dubos-wLh GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.8 99.0 GSM142624 MC002_ATH1_A1.2-dubos-wtx GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.7 99.0 GSM133759 Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
140.5	99.9	GSM133304	RIKEN-NAKABAYASHI1B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
135.0	99.9	GSM133303	RIKEN-NAKABAYASHI1A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
108.0	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
85.7	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
81.4	99.9	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
79.5	99.9	GSM10456	WT Post-Mature Green Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
79.3	99.9	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
65.2	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
62.9	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
61.6	99.8	GSM10454	WT Post-Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
60.2	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.9	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
50.9	99.8	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
43.0	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.9	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
39.9	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.5	99.8	GSM10451	WT Mature Green Seed 1	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
38.3	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
38.3	99.8	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
35.4	99.7	GSM131702	ATGE_82_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
34.3	99.7	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
32.8	99.7	GSM131701	ATGE_82_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
31.8	99.7	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
31.4	99.7	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
28.1	99.7	GSM153927	ahg1-1 rep2	GSE6638	Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
26.9	99.7	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
25.1	99.6	GSM131700	ATGE_82_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
24.3	99.6	GSM133309	RIKEN-NAKABAYASHI4B	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
20.2	99.6	GSM153928	ahg3-1 rep1	GSE6638	Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
20.0	99.6	GSM153929	ahg3-1 rep2	GSE6638	Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
19.2	99.6	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.7	99.5	GSM153926	ahg1-1 rep1	GSE6638	Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
18.2	99.5	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
18.2	99.5	GSM133117	RIKEN-YAMAUCHI1A	GSE5687	AtGenExpress: Different temperature treatment of seeds
16.4	99.5	GSM131706	ATGE_84_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
16.3	99.5	GSM131698	ATGE_81_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.4	99.5	GSM131699	ATGE_81_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
15.0	99.4	GSM131697	ATGE_81_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
14.4	99.4	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
14.2	99.4	GSM131705	ATGE_83_C	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
14.1	99.4	GSM131707	ATGE_84_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
13.9	99.4	GSM131708	ATGE_84_D	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
13.5	99.4	GSM131703	ATGE_83_A	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
12.6	99.3	E-MEXP-509-raw-cel-829148561
12.5	99.3	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
10.7	99.2	E-MEXP-1443-raw-cel-1581869573
10.0	99.2	GSM133308	RIKEN-NAKABAYASHI4A	GSE5700	AtGenExpress: Effect of ABA during seed imbibition
10.0	99.2	GSM153925	ABA control rep2	GSE6638	Expression data of germinating ahg1, ahg3 and WT seedling in the presence of ABA
9.9	99.1	GSM131704	ATGE_83_B	GSE5634	AtGenExpress: Developmental series (siliques and seeds)
9.7	99.1	GSM10453	WT Mature Green Seed 2	GSE680	Transcript Profiling of Arabidopsis Plant Life Cycle
9.6	99.1	GSM142625	MC002_ATH1_A1.3-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.5	99.1	GSM142642	MC002_ATH1_A7.2-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
9.5	99.1	GSM142643	MC002_ATH1_A7.3-dubos-wLh	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.8	99.0	GSM142624	MC002_ATH1_A1.2-dubos-wtx	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.7	99.0	GSM133759	Lindsey_1-9_heart-stage-cotyledon_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.026 1 GO:0006350 The synthesis of either RNA on a template of DNA or DNA on a template of RNA.

SF	Genes	GO ID	Process Name	Link to AmiGO
0.026	1	GO:0006350	The synthesis of either RNA on a template of DNA or DNA on a template of RNA.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.059 1 03020 RNA polymerase
0.026 1 00240 Pyrimidine metabolism
0.018 1 00230 Purine metabolism

SF	Genes	KEGG ID	Pathway name
0.059	1	03020	RNA polymerase
0.026	1	00240	Pyrimidine metabolism
0.018	1	00230	Purine 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	At3g57660
Gene name	NRPA1
Module size	5 genes
NF	0.71
%ile	89.8

Co-expression analysis

Gene ID At3g57660 Gene name NRPA1 Module size 5 genes NF 0.71 %ile 89.8

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

SFGenesGO IDProcess NameLink to AmiGO0.0261GO:0006350The synthesis of either RNA on a template of DNA or DNA on a template of RNA.

KEGG PATHWAY inferred to related to the module

SFGenesKEGG IDPathway nameLink to KEGG0.059103020RNA polymerase0.026100240Pyrimidine metabolism0.018100230Purine 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 At3g57660

Gene name NRPA1

Module size 5 genes

NF 0.71

%ile 89.8

: Transcription factor, : Binding protein, : Enzyme protein, : Other protein
: VF over 0.50, : over 0.25, : below 0.25

SF Genes GO ID Process Name Link to AmiGO
0.026 1 GO:0006350 The synthesis of either RNA on a template of DNA or DNA on a template of RNA.

SF Genes KEGG ID Pathway name Link to KEGG
0.059 1 03020 RNA polymerase
0.026 1 00240 Pyrimidine metabolism
0.018 1 00230 Purine 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