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

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).

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