Figure 4

ROC analysis to compare the ability of ChIP sites in variably sized windows to predict induced genes. Positives and negatives are taken as in Fig. 3. Number and definition of operative points is as in Fig. 3. The discrete curves lie on the same envelope, but the number of sites along the transcript (black curve) shows the best performance for all the sites definitions used (high stringency and low stringency ChIP-chip, ChIP-pet). The expression datasets are the cancer expression compendium and the study on primary estrogen receptor targets. In each experiment, the induced genes (positives) are taken as the 1% highest ranking transcripts. The remaining 99% are taken as the negatives. The same analyses using different definitions of sites (high stringency or ChIP-pet) are given in [see Additional file 4]. Further expression sets are analyzed in [see Additional file 5].