Fig. 4

Comparative analysis results of comparing timepoint 0h to 72h in the Inoue-Kreimer dataset. ap value distributions of candidates (top) and controls (bottom). QuASAR-MPRA is poorly calibrated, whereas MPRAnalyze and both mpralm modes follow the theoretical behavior (mixture of uniform and low values). b Direct comparison of MPRAnalyze to competing methods. Top panels show the biological effect size (log fold-change); Bottom panels show the statistical significance (BH-corrected p; dotted lines are 0.05 threshold). c Venn diagram for MPRAnalyze and mpralm (both modes). The numbers in each area are (top) the total number of sequences in the area, and (bottom) the number of decreasing-activity sequences (left) + and increasing-activity sequences (right). d Enrichment of transcription factor binding sites in differentially active sequences as determined by each method. Solid line represents threshold of 0.05. (see “Methods” for further details)