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Relative expression values were calculated after normalizing against the maximum expression value.
For each gene we firstly identified the maximum expression value recorded.
Firstly, pre-processed Affymetrix datasets were collapsed to the probeset with the maximum expression value for each gene using the Gene Set Enrichment Analysis software (details below).
Although values significantly higher than controls were recorded at 1, 3 and 6 h pt, the maximum expression value was obtained at 1 h pt.
When multiple probes map to the same gene, the maximum expression value is used.
We choose the maximum expression value as gene expression value if multiple probes illustrate the same gene expression.
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To reduce noise, we filtered the matrix to keep only significantly expressed (>5 FPKM in at least one experiment) and differentially expressed TFs (>2 fold difference between minimum and maximum expression values across all cell-lines).
The average and maximum expression values of each gene were calculated.
Results for average gene expression (E avg ) across the time periods are presented here; results do not differ when maximum expression values (E max ) are used.
Strain Lalvin EC-1118 showed a strong expression of OPT2 at T2 while other strains achieved maximum expression values during late fermentation stages (T3 or T4).
For each bin, the maximum expression values of the genes corresponding to the CpG probes were averaged for all patients (n = 40).
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