CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At3g48890

Gene name ATMP2

Module size 5 genes

NF 0.27

%ile 31.1

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
0.12 4.9 1.00 At3g48890 824050 ATMP2 putative progesterone-binding protein homolog (Atmp2) mRNA, O.I. H.G. S.X.
0.50 65.3 0.87 At3g54640 824629 TSA1 (TRYPTOPHAN SYNTHASE ALPHA CHAIN) Catalyzes the conversion of indole-3-glycerolphosphate to indole, the penultimate reaction in the biosynthesis of tryptophan. Functions as a heterocomplex with tryptophan synthase beta subunit (TSA2). O.I. H.G. S.X.
0.44 57.2 0.88 At1g10700 837613 ribose-phosphate pyrophosphokinase 3 / phosphoribosyl diphosphate synthetase 3 (PRS3) F:magnesium ion binding, ribose phosphate diphosphokinase activity;P:cellular biosynthetic process, nucleotide biosynthetic process, nucleoside metabolic process, ribonucleoside monophosphate biosynthetic process;C:chloroplast;BOMFAPV O.I. H.G. S.X.
0.43 55.3 0.86 At2g04400 814980 indole-3-glycerol phosphate synthase (IGPS) F:indole-3-glycerol-phosphate synthase activity;P:tryptophan biosynthetic process;C:chloroplast;BOAFP O.I. H.G. S.X.
0.40 50.8 0.87 At2g24180 816952 CYP71B6 (CYTOCHROME P450 71B6) cytochrome P450 monooxygenase O.I. H.G. S.X.

VF	%ile	CC	Gene ID	Repr. ID	Gene name	Func.	O.I.	H.G.	S.X.
0.12	4.9	1.00	At3g48890	824050	ATMP2	putative progesterone-binding protein homolog (Atmp2) mRNA,	O.I.	H.G.	S.X.
0.50	65.3	0.87	At3g54640	824629	TSA1 (TRYPTOPHAN SYNTHASE ALPHA CHAIN)	Catalyzes the conversion of indole-3-glycerolphosphate to indole, the penultimate reaction in the biosynthesis of tryptophan. Functions as a heterocomplex with tryptophan synthase beta subunit (TSA2).	O.I.	H.G.	S.X.
0.44	57.2	0.88	At1g10700	837613	ribose-phosphate pyrophosphokinase 3 / phosphoribosyl diphosphate synthetase 3 (PRS3)	F:magnesium ion binding, ribose phosphate diphosphokinase activity;P:cellular biosynthetic process, nucleotide biosynthetic process, nucleoside metabolic process, ribonucleoside monophosphate biosynthetic process;C:chloroplast;BOMFAPV	O.I.	H.G.	S.X.
0.43	55.3	0.86	At2g04400	814980	indole-3-glycerol phosphate synthase (IGPS)	F:indole-3-glycerol-phosphate synthase activity;P:tryptophan biosynthetic process;C:chloroplast;BOAFP	O.I.	H.G.	S.X.
0.40	50.8	0.87	At2g24180	816952	CYP71B6 (CYTOCHROME P450 71B6)	cytochrome P450 monooxygenase	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
342.6 100.0 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
223.3 100.0 GSM205430 met1-3_leaf_fourth-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
175.8 100.0 GSM205364 met1-3_leaf_second-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
109.3 99.9 GSM205428 met1-3_leaf_fourth-selfed generation_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
107.6 99.9 GSM205426 met1-3_leaf_second-selfed generation_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
105.7 99.9 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
94.2 99.9 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
66.5 99.8 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
59.6 99.8 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
57.6 99.8 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
55.4 99.8 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
55.1 99.8 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.4 99.8 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.0 99.8 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.9 99.8 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
51.9 99.8 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6 99.8 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
50.8 99.8 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
49.8 99.8 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
48.9 99.8 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.4 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
44.7 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
43.7 99.8 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.5 99.8 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.9 99.8 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.9 99.6 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.8 99.6 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.2 99.6 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
15.4 99.5 GSM133766 Lindsey_1-18_torpedo-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
342.6	100.0	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
223.3	100.0	GSM205430	met1-3_leaf_fourth-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
175.8	100.0	GSM205364	met1-3_leaf_second-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
109.3	99.9	GSM205428	met1-3_leaf_fourth-selfed generation_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
107.6	99.9	GSM205426	met1-3_leaf_second-selfed generation_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
105.7	99.9	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
94.2	99.9	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
66.5	99.8	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
59.6	99.8	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
57.6	99.8	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
55.4	99.8	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
55.1	99.8	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.4	99.8	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
53.0	99.8	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
52.9	99.8	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
51.9	99.8	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
51.6	99.8	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
50.8	99.8	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
49.8	99.8	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
48.9	99.8	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
46.4	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
44.7	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
43.7	99.8	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
41.5	99.8	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
39.9	99.8	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.9	99.6	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
24.8	99.6	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
23.2	99.6	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
15.4	99.5	GSM133766	Lindsey_1-18_torpedo-root_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
0.200 1 GO:0009156 The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a glycosamine consisting of a base linked to a ribose sugar esterified with phosphate on its glycose moiety.
0.182 1 GO:0009165 The chemical reactions and pathways resulting in the formation of nucleotides, any 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).
0.182 1 GO:0044249 The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

SF	Genes	GO ID	Process Name
0.200	1	GO:0009156	The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a glycosamine consisting of a base linked to a ribose sugar esterified with phosphate on its glycose moiety.
0.182	1	GO:0009165	The chemical reactions and pathways resulting in the formation of nucleotides, any 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).
0.182	1	GO:0044249	The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.089 2 00400 Phenylalanine, tyrosine and tryptophan biosynthesis
0.041 1 00260 Glycine, serine and threonine metabolism
0.022 2 01063 Biosynthesis of alkaloids derived from shikimate pathway
0.016 2 01061 Biosynthesis of phenylpropanoids
0.013 2 01070 Biosynthesis of plant hormones
0.003 2 01100 Metabolic pathways

SF	Genes	KEGG ID	Pathway name
0.089	2	00400	Phenylalanine, tyrosine and tryptophan biosynthesis
0.041	1	00260	Glycine, serine and threonine metabolism
0.022	2	01063	Biosynthesis of alkaloids derived from shikimate pathway
0.016	2	01061	Biosynthesis of phenylpropanoids
0.013	2	01070	Biosynthesis of plant hormones
0.003	2	01100	Metabolic pathways

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	At3g48890
Gene name	ATMP2
Module size	5 genes
NF	0.27
%ile	31.1

Co-expression analysis

Gene ID At3g48890 Gene name ATMP2 Module size 5 genes NF 0.27 %ile 31.1

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

Inter-species module comparison

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

Gene ID At3g48890

Gene name ATMP2

Module size 5 genes

NF 0.27

%ile 31.1

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

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