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An Improved, Bias-Reduced Probabilistic Functional Gene Network of Baker's Yeast, Saccharomyces cerevisiae

Figure 4

Summary of benchmarking for the YeastNet v. 2 integrated functional gene network, along with the functional linkage sets derived from the ten individual types of data.

Precision and recall of yeast genes are calculated using the unbiased MIPS functional linkage reference set, as in Figure 3C. Gene pairs in each set were ranked by LLS scores, then cumulative precision and recall were calculated for each successive bin of 1,000 gene pairs (each symbol indicates a bin). The confidence measures for each individual data type can be seen to rank the gene pairs effectively. YeastNet v. 2 shows high overall performance, with the integration of the heterogeneous genomics data improving both reliability and completeness of the overall model.

Figure 4

doi: https://doi.org/10.1371/journal.pone.0000988.g004