Fig. 4: The mAP framework applied to proteomic and mRNA profiling.

A mAP is calculated to assess the phenotypic activity of compounds by replicate retrievability against controls in matching Cell Painting and nELISA profiling data. B A combined view of the data from (A) is presented, showing phenotypic activity retrieval for both assays. C mAP is calculated to assess the phenotypic consistency by retrieving phenotypically active compounds annotated with the same gene target in matching Cell Painting and nELISA profiling data (note: the nELISA panel includes 191 targets including cytokines, chemokines, and growth factors which are not expected to respond well in these convenience samples from a prior study, because there is no immune stimulation and the A549 cells used have limited secretory capacity). D A combined view of the data from (C) is presented, showing phenotypic consistency retrieval for both assays. E mAP is calculated to assess the mRNA profile-based phenotypic activity of a mismatched CRISPRi guide from a Perturb-seq experiment (y-axis) and correlate it with the guide’s activity relative to a perfectly matching guide for that gene (x-axis). A linear model fit is shown in black with gray error bands showing the 95% confidence interval. F A subset of the data from (E) is presented, with several genes highlighted individually to demonstrate the variation from gene to gene. mAP p-values were estimated using a one-sided permutation test and adjusted for multiple comparisons by Benjamini–Hochberg procedure. Percent retrieved indicates the percentage of scores with p-value below 0.05. Source data are provided as a Source Data file.