Fig. 3

Logistic regression with covariates accurately calls motifs for ChIPed TFs in ENCODE experiments. a Plot of the rank for the enrichment score of the ChIPed TF’s motif in 23 ENCODE H1-hESC ChIP-seq experiments, across multiple score-based MEA. b Plot of the rank for the enrichment score of the ChIPed TF’s motif across multiple ENCODE cell lines. Only cell lines with more than 10 experiments analyzed are represented, as well as a separate category summarizing all cell lines. c Bar plot of Fisher exact test significance for enrichment of ENCODE warning flags among 36 (out of 582 eligible) experiments for which logistic regression with covariates failed to call the true ChIP-ed TF as significant, showing partial characterization of ChIP-seq antibodies as a significantly enriched warning term (Fisher exact test p-value = 6.8e-5, FDR = 1.563e-3)