Figure 4.

Performance of our algorithm on publicly available Chip² data [2] is evaluated using the Yeast Proteome Database collection of transcription factor targets [28,29] and compared with another popular means of computing p values [2]. (a) Receiver-operating characteristic curves for our method (black, 'Chipper') and that of Lee et al. [2] (green, 'Lee') using three replicate experiments for the transcription factor Ino4, made publicly available by Lee et al. (b) Sensitivity as a function of significance threshold. The broken line represents the performance of choosing potential targets at random. (c,d) Analogous curves for the transcription factor Sko1. FP, false positive; TP, true positive.