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

Additional data file 1:

Differentially expressed genes in the central metabolism of A. nidulans between the replicated experiments on glucose and ethanol, revealed by the logit-t method (see Additional data file 9 [Table S6] for a full list of genes. Upregulated and downregulated genes are represented in red and green, respectively. Fold changes greater than 10 are highlighted in bold.

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Additional data file 2:

Differentially expressed genes in the central metabolism of A. nidulans between the replicated experiments on glycerol and ethanol, revealed by the logit-t method (see Additional data file 9 [Table S7] for a full list of genes. Upregulated and downregulated genes are represented in red and green, respectively. Fold changes greater than 10 are highlighted in bold.

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Additional data file 3:

Differentially expressed genes in the central metabolism of A. nidulans between the replicated experiments on glucose and glycerol, revealed by the logit-t method (see Additional data file 9 [Table S8] for a full list of genes. Upregulated and downregulated genes are represented in red and green, respectively. Fold changes greater than 10 are highlighted in bold.

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Additional data file 4:

Reporter metabolites and enzymes comprising the 'small' subnetwork identified by comparing expression data on glucose and ethanol (represented in blue). Also shown are the top 15 high-scoring reporter metabolites.

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Additional data file 5:

Reporter metabolites and enzymes comprising the 'small' subnetwork identified by comparing expression data on glycerol and ethanol (represented in blue). Also shown are the top 15 high-scoring reporter metabolites.

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Additional data file 6:

Reporter metabolites and enzymes comprising the 'small' subnetwork identified by comparing expression data on glucose and glycerol (represented in blue). Also shown are the top 15 high-scoring reporter metabolites.

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Additional data file 7:

Table S1 lists the reactions comprising the metabolic reconstruction developed for A. nidulans. Each reaction is associated to an ORF within the genome of A. nidulans (when available), and to the EC number of the corresponding enzyme (when available). Table S2 lists metabolites, abbreviations used, and full names. (In the abbreviations, the suffixes m, g, and e stand for metabolites localized in the mitochondria, glyoxysomes and extracellular medium, respectively. No suffix was added to cytosolic metabolites.)

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Additional data file 8:

Tables S3, S4, and S5 give normalized intensities considering the replicated experiments on glucose and ethanol, on glycerol and ethanol, and on glucose and glycerol, respectively.

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Additional data file 9:

Tables S6, S7 and S8 list differentially expressed genes between the replicated experiments on glucose and ethanol, revealed by the logit-t method. The genes are sorted according to ascending P value from the statistical analysis. The average fold changes of expression between ethanol and glucose (Table S6), between ethanol and glycerol (Table S7), and between glycerol and glucose (Table S8) are also presented (a fold change equal to 2 [-2] indicates a twofold upregulation [downregulation] in ethanol relative to glucose [Table S6], in ethanol relative to glycerol [Table S7], or in glycerol relative to glucose [Table S8]).

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Additional data file 10:

Tables S9 and S10 present the classifications of the upregulated and downregulated genes, respectively, given in Table 2 into GO categories (provided by CADRE), according to the three most important biological processes and molecular functions.

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Additional data file 11:

Table S11 gives the normalized intensities considering all of the categories of replicated experiments (glucose, glycerol, and ethanol). Table S12 provides P values from the ANOVA test between all categories of replicated experiments (glucose, glycerol, and ethanol). The genes are sorted according to ascending P value.

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Additional data file 12:

Table S13 summarizes gene clusters identified by applying ClusterLustre to the genes that were found to be significantly changed in the ANOVA test.

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Additional data file 13:

Tables S14, S15, and S16 provide lists of enzymes and transporters comprising the 'large' subnetwork, obtained by comparing expression data on glucose and ethanol, on glycerol and ethanol, and on glucose and glycerol, respectively.

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Additional data file 14:

Table S17 summarizes the classification of the genes included in the 'small' highly correlated subnetworks into GO categories (provided by CADRE), according to the three most important biological processes and molecular functions.

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