CoP: Co-expressed Biological Processes

Co-expression analysis

Gene ID At1g10070

Gene name ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2)

Module size 8 genes

NF 0.64

%ile 85.1

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
1.00 100.0 1.00 At1g10070 837543 ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2) Encodes a chloroplast branched-chain amino acid aminotransferase. Complements the yeast leu/iso-leu/val auxotrophy mutant. O.I. H.G. S.X.
0.82 90.9 0.77 At1g08630 837385 THA1 (Threonine Aldolase 1) Encodes a threonine aldolase, involved in threonine degradation to glycine. Primarily expressed in seeds and seedlings. O.I. H.G. S.X.
0.82 90.9 0.79 At1g21400 838739 2-oxoisovalerate dehydrogenase, putative / 3-methyl-2-oxobutanoate dehydrogenase, putative / branched-chain alpha-keto acid dehydrogenase E1 alpha subunit, putative F:oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity;P:metabolic process;C:unknown;BOMFPA O.I. H.G. S.X.
0.67 81.6 0.81 At3g47340 823888 ASN1 (GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1) encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell. O.I. H.G. S.X.
0.59 74.7 0.86 At1g03090 838362 MCCA MCCA is the biotinylated subunit of the dimer MCCase, which is involved in leucine degradation. Both subunits are nuclear coded and the active enzyme is located in the mitochondrion. O.I. H.G. S.X.
0.46 59.8 0.77 At1g06570 837168 PDS1 (PHYTOENE DESATURATION 1) Mutation of the PDS1 locus disrupts the activity of p-hydroxyphenylpyruvate dioxygenase (HPPDase), the first committed step in the synthesis of both plastoquinone and tocopherols in plants. O.I. H.G. S.X.
0.44 57.2 0.84 At3g45300 823668 IVD (ISOVALERYL-COA-DEHYDROGENASE) Encodes isovaleryl-coenzyme a dehydrogenase. O.I. H.G. S.X.
0.44 57.2 0.76 At3g13450 820547 DIN4 (DARK INDUCIBLE 4) branched chain alpha-keto acid dehydrogenase E1 beta 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	At1g10070	837543	ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2)	Encodes a chloroplast branched-chain amino acid aminotransferase. Complements the yeast leu/iso-leu/val auxotrophy mutant.	O.I.	H.G.	S.X.
0.82	90.9	0.77	At1g08630	837385	THA1 (Threonine Aldolase 1)	Encodes a threonine aldolase, involved in threonine degradation to glycine. Primarily expressed in seeds and seedlings.	O.I.	H.G.	S.X.
0.82	90.9	0.79	At1g21400	838739	2-oxoisovalerate dehydrogenase, putative / 3-methyl-2-oxobutanoate dehydrogenase, putative / branched-chain alpha-keto acid dehydrogenase E1 alpha subunit, putative	F:oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity;P:metabolic process;C:unknown;BOMFPA	O.I.	H.G.	S.X.
0.67	81.6	0.81	At3g47340	823888	ASN1 (GLUTAMINE-DEPENDENT ASPARAGINE SYNTHASE 1)	encodes a glutamine-dependent asparagine synthetase, the predicted ASN1 peptide contains a purF-type glutamine-binding domain, and is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. Expression is induced within 3 hours of dark treatment, in senescing leaves and treatment with exogenous photosynthesis inhibitor. Induction of gene expression was suppressed in excised leaves supplied with sugar. The authors suggest that the gene's expression pattern is responding to the level of sugar in the cell.	O.I.	H.G.	S.X.
0.59	74.7	0.86	At1g03090	838362	MCCA	MCCA is the biotinylated subunit of the dimer MCCase, which is involved in leucine degradation. Both subunits are nuclear coded and the active enzyme is located in the mitochondrion.	O.I.	H.G.	S.X.
0.46	59.8	0.77	At1g06570	837168	PDS1 (PHYTOENE DESATURATION 1)	Mutation of the PDS1 locus disrupts the activity of p-hydroxyphenylpyruvate dioxygenase (HPPDase), the first committed step in the synthesis of both plastoquinone and tocopherols in plants.	O.I.	H.G.	S.X.
0.44	57.2	0.84	At3g45300	823668	IVD (ISOVALERYL-COA-DEHYDROGENASE)	Encodes isovaleryl-coenzyme a dehydrogenase.	O.I.	H.G.	S.X.
0.44	57.2	0.76	At3g13450	820547	DIN4 (DARK INDUCIBLE 4)	branched chain alpha-keto acid dehydrogenase E1 beta	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 GSM253646 Low_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
28.0 99.7 GSM253645 High_Mo_seg_pool_Ler_col_F2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
25.8 99.7 GSM253648 Col-0-1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
25.8 99.7 GSM253649 Col-0-2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
21.9 99.6 GSM143299 High_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.4 99.6 GSM133774 Lindsey_1-26_torpedo-meristem_Rep2_ATH1 GSE5730 Transcriptional profiling of laser-capture micro-dissected embryonic tissues
21.2 99.6 GSM184537 Whole roots 2hr KCl control treated then frozen, biological rep1 GSE7631 Cell-specific nitrogen responses in the Arabidopsis root
17.7 99.5 GSM253647 Col-0 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
17.6 99.5 GSM143307 Low_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.8 99.5 GSM143306 High_Na_seg_pool_tsu_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.3 99.4 GSM143298 Low_Na_seg_pool_ts_col_F2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.7 99.4 E-ATMX-1-raw-cel-1112746095
13.2 99.4 GSM143300 Ts_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.6 99.3 GSM253652 Ler 2 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.4 99.3 GSM143302 Ts_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.4 99.3 GSM253651 Ler 1 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
11.3 99.3 GSM143310 Tsu_genomic_hyb_1 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.2 99.2 GSM143308 Tsu_genomic_hyb_3 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.1 99.2 GSM143301 Ts_genomic_hyb_2 GSE6203 Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.0 99.2 GSM253650 Ler 3 GSE10039 Low_Mo_Arabidopsis_mapping_MOT1
8.7 99.0 GSM205432 Col_ leaf_ wildtype_rep01 GSE8279 Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

Std2 GX	%ile	GSM ID	Assay name	GSE ID	Experiment title
33.9	99.7	GSM253646	Low_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
28.0	99.7	GSM253645	High_Mo_seg_pool_Ler_col_F2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.8	99.7	GSM253648	Col-0-1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
25.8	99.7	GSM253649	Col-0-2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
21.9	99.6	GSM143299	High_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
21.4	99.6	GSM133774	Lindsey_1-26_torpedo-meristem_Rep2_ATH1	GSE5730	Transcriptional profiling of laser-capture micro-dissected embryonic tissues
21.2	99.6	GSM184537	Whole roots 2hr KCl control treated then frozen, biological rep1	GSE7631	Cell-specific nitrogen responses in the Arabidopsis root
17.7	99.5	GSM253647	Col-0 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
17.6	99.5	GSM143307	Low_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
15.8	99.5	GSM143306	High_Na_seg_pool_tsu_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
14.3	99.4	GSM143298	Low_Na_seg_pool_ts_col_F2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
13.7	99.4	E-ATMX-1-raw-cel-1112746095
13.2	99.4	GSM143300	Ts_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.6	99.3	GSM253652	Ler 2	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.4	99.3	GSM143302	Ts_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.4	99.3	GSM253651	Ler 1	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
11.3	99.3	GSM143310	Tsu_genomic_hyb_1	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.2	99.2	GSM143308	Tsu_genomic_hyb_3	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.1	99.2	GSM143301	Ts_genomic_hyb_2	GSE6203	Rus_etal_High_Na_Arabidopsis_accessions_mapping_HKT1
11.0	99.2	GSM253650	Ler 3	GSE10039	Low_Mo_Arabidopsis_mapping_MOT1
8.7	99.0	GSM205432	Col_ leaf_ wildtype_rep01	GSE8279	Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation

Biological processes inferred to relate to the module

SF Genes GO ID Process Name Link to AmiGO
0.222 1 GO:0009063 The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
0.222 1 GO:0043617 A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of sucrose.
0.200 1 GO:0006567 The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

SF	Genes	GO ID	Process Name
0.222	1	GO:0009063	The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
0.222	1	GO:0043617	A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of sucrose.
0.200	1	GO:0006567	The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

KEGG PATHWAY inferred to related to the module

SF Genes KEGG ID Pathway name Link to KEGG
0.186 4 00280 Valine, leucine and isoleucine degradation
0.087 1 00770 Pantothenate and CoA biosynthesis
0.069 1 00966 Glucosinolate biosynthesis

SF	Genes	KEGG ID	Pathway name
0.186	4	00280	Valine, leucine and isoleucine degradation
0.087	1	00770	Pantothenate and CoA biosynthesis
0.069	1	00966	Glucosinolate biosynthesis

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	At1g10070
Gene name	ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2)
Module size	8 genes
NF	0.64
%ile	85.1

Co-expression analysis

Gene ID At1g10070 Gene name ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2) Module size 8 genes NF 0.64 %ile 85.1

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

SFGenesKEGG IDPathway nameLink to KEGG0.186400280Valine, leucine and isoleucine degradation0.087100770Pantothenate and CoA biosynthesis0.069100966Glucosinolate biosynthesis

Inter-species module comparison

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

Gene ID At1g10070

Gene name ATBCAT-2 (ARABIDOPSIS THALIANA BRANCHED-CHAIN AMINO ACID TRANSAMINASE 2)

Module size 8 genes

NF 0.64

%ile 85.1

: 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
0.186 4 00280 Valine, leucine and isoleucine degradation
0.087 1 00770 Pantothenate and CoA biosynthesis
0.069 1 00966 Glucosinolate biosynthesis

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