CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At5g60540

Gene name PDX2 (PYRIDOXINE BIOSYNTHESIS 2)

Module size 5 genes

NF 0.03

%ile 1.6

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
1.00 100.0 1.00 At5g60540 836175 PDX2 (PYRIDOXINE BIOSYNTHESIS 2) Encodes a protein predicted to function in tandem with PDX1 to form glutamine amidotransferase complex with involved in vitamin B6 biosynthesis. PDX2 is predicted to function as glutaminase within the complex. O.I. H.G. S.X.
0.36 43.6 0.86 At5g62200 836341 embryo-specific protein-related F:molecular_function unknown;P:biological_process unknown;C:plasma membrane, anchored to membrane;P O.I. H.G. S.X.
0.07 1.9 0.84 At3g07640 819955 unknown protein F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P O.I. H.G. S.X.
0.02 0.4 0.85 At3g07630 819954 ADT2 (arogenate dehydratase 2) Encodes a plastid-localized arogenate dehydratase involved in phenylalanine biosynthesis. Not less than six genes encoding ADT were identiﬁed in the Arabidopsis genome: ADT1 [At1g11790]; ADT2 [At3g07630]; ADT3 [At2g27820]; ADT4 [At3g44720]; ADT5 [At5g22630]; and ADT6 [At1g08250]. O.I. H.G. S.X.
0.01 0.2 0.84 At3g15660 820809 GRX4 (GLUTAREDOXIN 4) F:metal ion binding;P:cell redox homeostasis;C:mitochondrion;OBMPFA 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	At5g60540	836175	PDX2 (PYRIDOXINE BIOSYNTHESIS 2)	Encodes a protein predicted to function in tandem with PDX1 to form glutamine amidotransferase complex with involved in vitamin B6 biosynthesis. PDX2 is predicted to function as glutaminase within the complex.	O.I.	H.G.	S.X.
0.36	43.6	0.86	At5g62200	836341	embryo-specific protein-related	F:molecular_function unknown;P:biological_process unknown;C:plasma membrane, anchored to membrane;P	O.I.	H.G.	S.X.
0.07	1.9	0.84	At3g07640	819955	unknown protein	F:molecular_function unknown;P:biological_process unknown;C:cellular_component unknown;P	O.I.	H.G.	S.X.
0.02	0.4	0.85	At3g07630	819954	ADT2 (arogenate dehydratase 2)	Encodes a plastid-localized arogenate dehydratase involved in phenylalanine biosynthesis. Not less than six genes encoding ADT were identiﬁed in the Arabidopsis genome: ADT1 [At1g11790]; ADT2 [At3g07630]; ADT3 [At2g27820]; ADT4 [At3g44720]; ADT5 [At5g22630]; and ADT6 [At1g08250].	O.I.	H.G.	S.X.
0.01	0.2	0.84	At3g15660	820809	GRX4 (GLUTAREDOXIN 4)	F:metal ion binding;P:cell redox homeostasis;C:mitochondrion;OBMPFA	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
33.9 99.7 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
18.1 99.5 GSM133762 Lindsey_1-14_torpedo-root_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
16.5 99.5 GSM47021 Col-0 11 GSE2473 Small RNA biogenesis mutants
16.0 99.5 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5 99.4 GSM226530 LCOLUMELLASB GSE8934 A high resolution organ expression map reveals novel expression patterns and predicts cellular function
14.1 99.4 GSM133760 Lindsey_1-12_heart-stage-root_Rep3_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.9 99.4 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.7 99.3 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
12.5 99.3 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
12.2 99.3 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.2 99.2 GSM242962 Mock day 7 (day7E2) GSE9605 Target genes of AGAMOUS during early flower development in Arabidopsis
11.1 99.2 GSM205435 Col_ leaf_ wildtype_rep02 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.0 99.2 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
10.8 99.2 GSM143309 Tsu_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.8 99.2 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.7 99.2 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.7 99.2 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.6 99.2 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.3 99.2 GSM242961 Mock day 7 (day7E1) GSE9605 Target genes of AGAMOUS during early flower development in Arabidopsis
10.2 99.2 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0 99.2 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9 99.1 E-MEXP-148-raw-cel-350528647
9.8 99.1 E-ATMX-13-raw-cel-1556149823
9.7 99.1 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.6 99.1 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.6 99.1 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.6 99.1 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
9.6 99.1 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4 99.1 GSM133776 Lindsey_1-1_globular-apical_Rep1_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.2 99.1 E-MEXP-148-raw-cel-350529179
9.2 99.1 GSM47027 dcl1-7 17 GSE2473 Small RNA biogenesis mutants
9.1 99.1 GSM47019 Ler 9 GSE2473 Small RNA biogenesis mutants
9.0 99.1 GSM47022 Col-0 12 GSE2473 Small RNA biogenesis mutants
8.9 99.0 E-MEXP-682-raw-cel-922397662
8.6 99.0 GSM142634 MC002_ATH1_A4.3-dubos-6kc GSE6151 The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.6 99.0 E-MEXP-682-raw-cel-922397696

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
33.9	99.7	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
18.1	99.5	GSM133762	Lindsey_1-14_torpedo-root_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
16.5	99.5	GSM47021	Col-0 11	GSE2473	Small RNA biogenesis mutants
16.0	99.5	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.5	99.4	GSM226530	LCOLUMELLASB	GSE8934	A high resolution organ expression map reveals novel expression patterns and predicts cellular function
14.1	99.4	GSM133760	Lindsey_1-12_heart-stage-root_Rep3_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
13.9	99.4	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
12.7	99.3	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
12.5	99.3	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
12.2	99.3	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.2	99.2	GSM242962	Mock day 7 (day7E2)	GSE9605	Target genes of AGAMOUS during early flower development in Arabidopsis
11.1	99.2	GSM205435	Col_ leaf_ wildtype_rep02	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation
11.0	99.2	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
10.8	99.2	GSM143309	Tsu_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.8	99.2	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.7	99.2	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.7	99.2	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.6	99.2	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.3	99.2	GSM242961	Mock day 7 (day7E1)	GSE9605	Target genes of AGAMOUS during early flower development in Arabidopsis
10.2	99.2	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
10.0	99.2	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.9	99.1	E-MEXP-148-raw-cel-350528647
9.8	99.1	E-ATMX-13-raw-cel-1556149823
9.7	99.1	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.6	99.1	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.6	99.1	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.6	99.1	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
9.6	99.1	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
9.4	99.1	GSM133776	Lindsey_1-1_globular-apical_Rep1_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
9.2	99.1	E-MEXP-148-raw-cel-350529179
9.2	99.1	GSM47027	dcl1-7 17	GSE2473	Small RNA biogenesis mutants
9.1	99.1	GSM47019	Ler 9	GSE2473	Small RNA biogenesis mutants
9.0	99.1	GSM47022	Col-0 12	GSE2473	Small RNA biogenesis mutants
8.9	99.0	E-MEXP-682-raw-cel-922397662
8.6	99.0	GSM142634	MC002_ATH1_A4.3-dubos-6kc	GSE6151	The mechanisms involved in the interplay between dormancy and secondary growth in Arabidopsis
8.6	99.0	E-MEXP-682-raw-cel-922397696

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.250 1 GO:0042819 The chemical reactions and pathways resulting in the formation of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
0.200 1 GO:0008615 The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
0.154 1 GO:0009094 The chemical reactions and pathways resulting in the formation of L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.

SF	Genes	GO ID	Process Name
0.250	1	GO:0042819	The chemical reactions and pathways resulting in the formation of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
0.200	1	GO:0008615	The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
0.154	1	GO:0009094	The chemical reactions and pathways resulting in the formation of L-phenylalanine, the L-enantiomer of 2-amino-3-phenylpropanoic acid, i.e. (2S)-2-amino-3-phenylpropanoic acid.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.154 1 00750 Vitamin B6 metabolism

SF	Genes	KEGG ID	Pathway name	Link to KEGG
0.154	1	00750	Vitamin B6 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	At5g60540
Gene name	PDX2 (PYRIDOXINE BIOSYNTHESIS 2)
Module size	5 genes
NF	0.03
%ile	1.6

Co-expression analysis

Gene ID At5g60540 Gene name PDX2 (PYRIDOXINE BIOSYNTHESIS 2) Module size 5 genes NF 0.03 %ile 1.6

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 KEGG0.154100750Vitamin B6 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 At5g60540

Gene name PDX2 (PYRIDOXINE BIOSYNTHESIS 2)

Module size 5 genes

NF 0.03

%ile 1.6

: 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
0.154 1 00750 Vitamin B6 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