CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g52090

Gene name NRPB11

Module size 5 genes

NF 0.34

%ile 44.6

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
0.27 26.2 1.00 At3g52090 824372 NRPB11 Non-catalytic subunit common to nuclear DNA-dependent RNA polymerases II, IV and V; homologous to budding yeast RPB11 and the E. oli RNA polymerase alpha subunit. O.I. H.G. S.X.
0.80 89.8 0.93 At4g02610 828226 tryptophan synthase, alpha subunit, putative F:tryptophan synthase activity;P:tryptophan biosynthetic process;C:chloroplast;BOAFPM O.I. H.G. S.X.
0.38 46.7 0.93 At5g58240 835936 bis(5'-adenosyl)-triphosphatase, putative Encodes a Fhit protein. Has nucleoside phosphoramidase and adenylylsulfatase activities. O.I. H.G. S.X.
0.29 30.3 0.93 At2g25570 817096 binding F:binding;P:biological_process unknown;C:unknown;BOMPVF O.I. H.G. S.X.
0.23 19.3 0.93 At1g73820 843718 Ssu72-like family protein F:phosphoprotein phosphatase activity;P:mRNA processing;C:chloroplast;MFPO O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.27	26.2	1.00	At3g52090	824372	NRPB11	Non-catalytic subunit common to nuclear DNA-dependent RNA polymerases II, IV and V; homologous to budding yeast RPB11 and the E. oli RNA polymerase alpha subunit.	O.I.	H.G.	S.X.
0.80	89.8	0.93	At4g02610	828226	tryptophan synthase, alpha subunit, putative	F:tryptophan synthase activity;P:tryptophan biosynthetic process;C:chloroplast;BOAFPM	O.I.	H.G.	S.X.
0.38	46.7	0.93	At5g58240	835936	bis(5'-adenosyl)-triphosphatase, putative	Encodes a Fhit protein. Has nucleoside phosphoramidase and adenylylsulfatase activities.	O.I.	H.G.	S.X.
0.29	30.3	0.93	At2g25570	817096	binding	F:binding;P:biological_process unknown;C:unknown;BOMPVF	O.I.	H.G.	S.X.
0.23	19.3	0.93	At1g73820	843718	Ssu72-like family protein	F:phosphoprotein phosphatase activity;P:mRNA processing;C:chloroplast;MFPO	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
205.5 100.0 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
165.3 100.0 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
156.1 99.9 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
155.6 99.9 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
140.5 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
130.7 99.9 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
130.2 99.9 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
119.3 99.9 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
114.0 99.9 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
112.0 99.9 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
106.9 99.9 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
103.6 99.9 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
98.1 99.9 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
81.9 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
71.6 99.9 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.0 99.8 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
61.1 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
52.5 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
49.1 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.0 99.8 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
47.8 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
46.3 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.5 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.2 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.3 99.8 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.4 99.7 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
30.4 99.7 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.3 99.5 GSM133945 Murray_2-1_T0-APH_Rep1_ATH1 GSE5747 Genome-wide cell cycle studies
11.8 99.3 GSM184923 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2 GSE7641 Expression analysis of root cell-types after treatment with salt
10.9 99.2 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.8 99.2 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
8.7 99.0 GSM184922 Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1 GSE7641 Expression analysis of root cell-types after treatment with salt

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
205.5	100.0	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
165.3	100.0	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
156.1	99.9	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
155.6	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
140.5	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
130.7	99.9	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
130.2	99.9	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
119.3	99.9	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
114.0	99.9	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
112.0	99.9	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
106.9	99.9	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
103.6	99.9	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
98.1	99.9	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
81.9	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
71.6	99.9	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
62.0	99.8	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
61.1	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
52.5	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
49.1	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
49.0	99.8	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
47.8	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
46.3	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
44.5	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
42.2	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.3	99.8	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
34.4	99.7	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
30.4	99.7	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
16.3	99.5	GSM133945	Murray_2-1_T0-APH_Rep1_ATH1	GSE5747	Genome-wide cell cycle studies
11.8	99.3	GSM184923	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2	GSE7641	Expression analysis of root cell-types after treatment with salt
10.9	99.2	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
10.8	99.2	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
8.7	99.0	GSM184922	Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1	GSE7641	Expression analysis of root cell-types after treatment with salt

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.167 1 GO:0009117 The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
0.080 1 GO:0000162 The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
0.069 1 GO:0006397 Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.

SF	Genes	GO ID	Process Name
0.167	1	GO:0009117	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
0.080	1	GO:0000162	The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
0.069	1	GO:0006397	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.059 1 03020 RNA polymerase
0.044 1 00400 Phenylalanine, tyrosine and tryptophan biosynthesis
0.041 1 00260 Glycine, serine and threonine metabolism
0.036 2 00230 Purine metabolism

SF	Genes	KEGG ID	Pathway name
0.059	1	03020	RNA polymerase
0.044	1	00400	Phenylalanine, tyrosine and tryptophan biosynthesis
0.041	1	00260	Glycine, serine and threonine metabolism
0.036	2	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

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Gene ID	At3g52090
Gene name	NRPB11
Module size	5 genes
NF	0.34
%ile	44.6

Co-expression analysis

Gene ID At3g52090 Gene name NRPB11 Module size 5 genes NF 0.34 %ile 44.6

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 KEGG0.059103020RNA polymerase0.044100400Phenylalanine, tyrosine and tryptophan biosynthesis0.041100260Glycine, serine and threonine metabolism0.036200230Purine 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 At3g52090

Gene name NRPB11

Module size 5 genes

NF 0.34

%ile 44.6

: 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 03020 RNA polymerase
0.044 1 00400 Phenylalanine, tyrosine and tryptophan biosynthesis
0.041 1 00260 Glycine, serine and threonine metabolism
0.036 2 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