Training phase variation effects on single gene (rank) predictions. The modified training compendiums were used to predict ranks of FL-target genes, ERG11, ERG6, ERG5, and non-target gene, SPT3, in five representative FL treatment experiments. First, gene ranks for 2 replicate experiments were averaged. Next, ranks from the original training compendium were subtracted from ranks derived from the modified training compendium, yielding rank changes, or RCs. Finally, RCs (y-axis) were plotted for five representative FL treatment experiments (x-axis) for each gene: (A) ERG11, (B) ERG6, (C) ERG5, and (D) SPT3. Positive RCs signified the gene rank improved with the addition of the corresponding deletion experiment data to the compendium. An RC of 0 indicated no change. A negative RC indicated rank increased or worsened.