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- Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans

Table 1

Biochemical conversions and transport processes, and number of ORFs associated with the metabolic reactions

Part of metabolism

Number of metabolic reactions

Number of previously annotated ORFs^a

Number of newly annotated ORFs

Total number of ORFs

Biochemical reactions

1,095 (681^b)

188

468

656

C-compound metabolism

463 (220)

166

262

Energy metabolism

20 (17)

Aminoacid metabolism

238 (171)

125

165

Nucleotide metabolism

144 (114)

Lipid metabolism

175 (122)

110

Secondary metabolism

42 (25)

Nitrogen and sulphur metabolism

8 (7)

Polymerization, assembly and maintenance

5 (5)

Transport processes

118 (113)

Total

1,213 (794)

194

472

666

Shown are the total number of biochemical conversions and transport processes included in the metabolic reconstruction for A. nidulans (number of unique reactions are given in parenthesis), and the number of ORFs (previously and newly annotated) associated with the metabolic reactions. The total number of unique ORFs in the metabolic network may be different from the sum of the number of ORFs in the different parts of the metabolism, because there are ORFs that encode functions in several parts of the metabolism. ^aAspergillus nidulans Database [9]. ^bSix nonenzymatic steps are included. ORF, open reading frame.

Table 2

Genes that are differentially expressed in the different pair-wise comparisons possible between the categories

Comparison	Total genes (up/down)	Metabolic genes (%)

Ethanol versus glucose	418 (249/169)	103 (25%)
Ethanol versus glycerol	206 (92/114)	58 (28%)
Glycerol versus glucose	71 (57/14)	12 (17%)

Shown are the number of genes that are differentially expressed in the different pair-wise comparisons possible between the categories, for a cutoff P value in the logit-t test of 0.01. The total number of genes is presented along with the number of upregulated (up) and downregulated (down) genes (shown in parenthesis). The number (and percentage) of metabolic genes identified within the differentially expressed genes is also shown.

Table 3

Classification of the genes in each cluster into GO categories

Cluster	Number of genes in cluster	Biological processes	Molecular functions

Cluster 1	280	Ribosome biogenesis Cytoplasm organization and biogenesis Ribosome biogenesis and assembly	RNA binding SnoRNA binding Nucleic acid binding
Cluster 2	146	Alcohol metabolism Monosaccharide metabolism Monosaccharide catabolism	Translation elongation factor activity Carbohydrate kinase activity Thryptophan synthase activity
Cluster 3	184	Karyogamy Karyogamy during conjugation with cellular fusion Glucan metabolism	DNA binding Protein kinase regulator activity Kinase regulator activity
Cluster 4	206		Peroxidase activity Oxidoreductase activity, acting on peroxide as acceptor
Cluster 5	92		Oxidoreductase activity Pyruvate dehydrogenase activity Pyruvate dehydrogenase (acetyl transferring) activity
Cluster 6	125	Generation of precursor metabolites and energy Energy derivation by oxidation of organic compounds Fatty acid β-oxidation	Oxidoreductase activity Triose-phosphate isomerase activity Allophanate hydrolase activity
Cluster 7	254	Cofactor metabolism Coenzyme metabolism Generation of precursor metabolites and energy	Hydrogen ion transporter activity Monovalent inorganic cation transporter activity Lyase activity
Cluster 8	212	Protein biosynthesis Cellular biosynthesis Macromolecule biosynthesis	Structural constituent of ribosome Structural molecule activity Peptidyltransferase activity

The genes in each cluster are classified into GO categories (provided by CADRE), according to the three most important biological processes and molecular functions. The fields with fewer than three categories correspond to cases in which the P values were above the cutoff selected in the GO term analysis. The sum of the number of genes in each cluster is not equal to the total number of differentially expressed genes (1,534) because 35 genes were discarded in the clustering analysis (see Analysis of transcriptome data, under Materials and methods).

Table 4

Highly regulated or reporter metabolites for the three possible pair-wise comparisons between the different carbon sources

Ethanol versus glucose	Ethanol versus glycerol	Glycerol versus glucose

Reporter metabolite	n	P	Reporter metabolite	n	P	Reporter metabolite	n	P

Acetyl coenzyme A (mitochondrial)	12	2.1E-06	Oxaloacetate	13	7.6E-05	N-Carbamoyl-L-aspartate	3	1.0E-03
Coenzyme A (mitochondrial)	14	2.6E-06	Coenzyme A (mitochondrial)	14	1.2E-04	Carbamoyl phosphate	5	1.7E-03
Glyoxylate (glyoxysomal)	3	1.8E-05	Glyoxylate (glyoxysomal)	3	2.1E-04	2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine	2	2.8E-03
Oxaloacetate	13	9.4E-05	Acetyl coenzyme A (mitochondrial)	12	2.7E-04	Glycogen	2	2.8E-03
Acetyl coenzyme A (glyoxysomal)	2	1.1E-04	Acetyl coenzyme A (glyoxysomal)	2	4.2E-04	Maltose	6	2.9E-03
Coenzyme A (glyoxysomal)	2	1.1E-04	Coenzyme A (glyoxysomal)	2	4.2E-04	Maltose (extracellular)	6	2.9E-03
Oxaloacetate (mitochondrial)	11	4.4E-04	Oxaloacetate (mitochondrial)	11	4.3E-04	L-glutamine	16	3.1E-03
Carnitine	2	4.9E-04	2-Oxoglutarate (mitochondrial)	9	4.9E-04	α-D-glucose 1-phosphate	4	3.4E-03
O-acetylcarnitine	2	4.9E-04	Citrate	1	5.6E-04	ATP	94	3.7E-03
Propanoyl-coenzyme A	3	6.1E-04	Phosphoenolpyruvate	6	8.5E-04	(R)-3-Hydroxy-3-methyl-2-oxobutanoate (mitochondrial)	2	4.4E-03
Maltose	6	7.0E-04	Fumarate (mitochondrial)	3	8.6E-04	(R)-2,3-dihydroxy-3-methylbutanoate (mitochondrial)	2	4.4E-03
Maltose (extracellular)	6	7.0E-04	α-D-glucose 1-phosphate	4	9.5E-04	Carbon dioxide	42	4.7E-03
O-acetylcarnitine (mitochondrial)	2	9.0E-04	Citrate (mitochondrial)	5	1.3E-03	S-acetyldihydrolipoamide (mitochondrial)	2	5.1E-03
Carnitine (mitochondrial)	2	9.0E-04	Carnitine	2	1.9E-03	Carbon dioxide (mitochondrial)	16	6.0E-03
O-acetylcarnitine (glyoxysomal)	2	9.0E-04	O-acetylcarnitine	2	1.9E-03	ADP	64	1.2E-02

Shown are highly regulated or reporter metabolites for the three possible pair-wise comparisons between the different carbon sources, according to Patil and Nielsen [23]. 'n' denotes the number of neighbors of the reporter metabolite (the number of reactions in which it participates).

Table 5

Enzymes and transporters in subnetworks

Ethanol versus glucose (26 reactions)	Ethanol versus glycerol (33 reactions)	Glycerol versus glucose (34 reactions)

6-Phosphofructokinase	1,3-β-Glucan synthase	5'-Phosphoribosylformyl glycinamidine synthetase
Acetyl-CoA hydrolase	Acetyl-CoA hydrolase	8-Amino-7-oxononanoate synthase
Aconitate hydratase (mitochondrial)	Acetyl-CoA synthase	Aldehyde dehydrogenase
Alcohol dehydrogenase	Aconitate hydratase (mitochondrial)	α,α-Trehalase
Aldehyde dehydrogenase	Adenylate kinase	α-Glucosidase
α-Glucosidase	Alanine-glyoxylate transaminase	α-Glucosidase
α-Glucosidase	Alcohol dehydrogenase	Aspartate-carbamoyltransferase
α-Glucosidase	Aldehyde dehydrogenase	Aspartate-carbamoyltransferase
Aspartate transaminase (mitochondrial)	Aspartate transaminase (mitochondrial)	B-ketoacyl-ACP synthase
Aspartate transaminase (mitochondrial)	Aspartate transaminase (mitochondrial)	Carbamoyl-phophate synthetase
ATP:citrate oxaloacetate-lyase	ATP:citrate oxaloacetate-lyase	Citrate synthase (mitochondrial)
Carnitine O-acetyltransferase	Carnitine O-acetyltransferase	Dihydrolipoamide S-acetyltransferase (mitochondrial)
Carnitine O-acetyltransferase (mitochondrial)	Carnitine O-acetyltransferase (mitochondrial)	Dihydroxy acid dehydratase (mitochondrial)
Carnitine/acyl carnitine carrier	Citrate synthase (mitochondrial)	Fatty-acyl-CoA synthase
Citrate synthase (mitochondrial)	Citrate synthase (mitochondrial)	Fatty-acyl-CoA synthase
Formate dehydrogenase	Formate dehydrogenase	Fructose-bisphosphatase
Fructose-bisphosphatase	Fumarate dehydratase (mitochondrial)	Glucan 1,3-β-glucosidase (extracellular)
Gluconolactonase (extracellular)	Glucose 6-phosphate 1-dehydrogenase	Glucose 6-phosphate 1-dehydrogenase
Glucose 6-phosphate 1-dehydrogenase	Glucose-6-phosphate isomerase	Glycerol 3-phosphate dehydrogenase (FAD dependent)
Glyceraldehyde 3-phosphate dehydrogenase	Glycerol 3-phosphate dehydrogenase (FAD dependent)	Glycerol dehydrogenase
Isocitrate lyase (glyoxysomal)	Glycerol dehydrogenase	Glycerol kinase
Glycerol kinase	Isocitrate lyase (glyoxysomal)	GTP cyclohydrolase I
Mannose-6-phosphate isomerase	Malate dehydrogenase (malic enzyme; NADP+)	Ketol-acid reductoisomerase (mitochondrial)
Phosphoenolpyruvate carboxykinase	Malate synthase (glyoxysomal)	Malate dehydrogenase (malic enzyme; NADP+)
Pyruvate kinase	Mannitol 2-dehydrogenase (NAD+)	Mannitol 2-dehydrogenase (NAD+)
Transketolase	Phosphoenolpyruvate carboxykinase	Mannitol 2-dehydrogenase (NADP+)
	Phosphoglucomutase	Phosphoenolpyruvate carboxykinase
	Phosphogluconate dehydrogenase (decarboxylating)	Phosphoribosylamine-glycine ligase
	Phosphorylase	Phosphorylase
	Pyruvate kinase	Pyruvate dehydrogenase (lipoamide) (mitochondrial)
	Transketolase	Pyruvate kinase
	UTP-glucose-1-phosphate uridylyltransferase	Ribulokinase
		UTP-glucose-1-phosphate uridylyltransferase

Shown is a list of the enzymes and transporters that participate in the 'small', highly correlated subnetworks for each pair-wise comparison between the three carbon sources investigated. Enzymes common to all reactions are highlighted in bold. Some enzymes appear more than once in the table, which means that they are isoenzymes and are encoded by different genes. CoA, coenzyme A.

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Tables - Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans

Tables
- Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans