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The Next Generation of Transcription Factor Binding Site Prediction

Figure 3

Performance comparison between TFFMs and weight matrices.

For the 96 ChIP-seq data sets obtaining an % for at least one method (using a genomic background), the ratio between the AUC value using a specific model and the best AUC obtained is plotted. The four types of models were used (1st-order TFFM, detailed TFFM, PWM, and DWM). By considering a similar performance between two methods when the AUC ratio is %, we plot at the top of the figure the region where the weight matrices (WMs) best perform, where the TFFMs best perform, and where they are similar. AUC ratios are ranked from the least to the most favourable to the TFFMs.

doi: https://doi.org/10.1371/journal.pcbi.1003214.g003