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Fig. 2 | BMC Genomics

Fig. 2

From: Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data

Fig. 2

Cell-cycle phase expression and performance of classifiers using TF-interaction data. a Expression profiles of genes at specific phases of the cell-cycle. The normalized expression levels of gene in each phase of the cell-cycle: G1 (red), S (yellow), S/G2 (green), G2/M (blue), and M/G1 (purple). Time (x-axis) is expressed in minutes and, for the purpose of displaying relative levels of expression over time, the expression (y-axis) of each gene was normalized between 0 and 1. Each figure shows the mean expression of the phase. Horizontal dotted lines divide the timescale into 25 min segment to highlight the difference in peak times between phases. b AUC-ROC values of SVM classifiers for whether a gene is cycling in any cell-cycle phases (general) or in a specific phase using TFs and TF-target interactions derived from each data set. The reported AUC-ROC for each classifier is the average AUC-ROC of 100 data subsets (see Methods). Darker red shading indicates an AUC-ROC closer to one (indicating a perfect classifier) while darker blue indicates an AUC-ROC closer to 0.5 (random guessing). c Classifiers constructed using the TF-target interactions from the ChIP, Deletion, or PWM1 data, but only for TFs that were also present in PBM data set. Other models perform better than the PBM-based model even when restricted to the same TFs as PBM. d Classifiers constructed using the TF-target interactions from the PWM1 data, but only for TFs that were also present in ChIP or Deletion data set. Note that PWM1 models preform as well when restricted to TFs used by smaller data sets

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