Fig. 3

Comparison of p53retriever with other p53 binding site datasets and tools. a Pie chart displaying p53retriever classification on a list of 81 regions commonly identified by 7 different ChIP-seq experiments [15]. b Left panel: pie chart displaying p53retriever classification on a list of 2250 regions identified by ChIP-exo [14]. Right panel: boxplot displaying for each grade assigned by p53retriever to ChIP-exo sequences, the distribution of the corresponding ChIP-exo occupancies, measured in [14]. n.g. = no grade given by p53retriever. c Pie chart displaying p53retriever classification on a list of 4416 regions identified by ChIP-seq in [17]. d p53 target gene lists from curated databases (Biobase and IPA) or from expression datasets (Doxo up: genes up-regulated upon doxorubicin treatment) were compared to the list of p53 promoter REs obtained with p53retriever. Presented in the bar graph are the predicted p53 REs grouped by the maximum functional grade identified by p53retriever in their promoter. e Comparison between p53 REs identified in human promoters by p53retriever, and the corresponding score given by Jaspar p53 PWM (MA0106.2), based on ChIPseq data. REs are divided in 5 groups along the horizontal axis, corresponding to the grade assigned by p53retriever. For each group, the distribution of the scores given by Jaspar PWM is represented as a violin plot, i.e., a box plot with a rotated kernel density plot on each side. Jaspar scores range from 0 (the RE is not identified) to 1 (the RE is optimal)