Figure 4.
A comparison of the ability of DNA-binding motifs derived from different in vitro experiments to explain in vivo binding patterns. (A) Receiver Operator Characteristic (ROC) curve for quantitating how well a DIP-chip derived PWM can predict the results of a ChIP-chip experiment. The best PWM defined by the 4-nM DIP-chip data was used to calculate this plot (Methods; Fig. 2). Identical analyses were performed on PWMs derived from SELEX, EMSA, and all DIP-chip PWMs. (B) Areas under the ROC curve for PWMs evaluated against the ChIP data. The 95% confidence interval for the EMSA Kd ROC AUC value was estimated by bootstrap resampling of the occupancy scores and enrichment values for the 22 ChIP-enriched features. For the DIP-chip defined PWMs, the PWM that scored best when evaluated against the DIP data itself is shown as a filled circle. Other PWMs that are within the confidence interval of the best when evaluated against the DIP data are shown as open circles. (C) Same as B, but with a zoomed-in ROC AUC scale.