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Fig. 4 | Genome Biology

Fig. 4

From: gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens

Fig. 4

Gene-specific phenotypes (GSPs) for pathogen entry estimated by gespeR from two distinct genome-wide Qiagen sub-libraries are biologically meaningful. a Scatterplots of reagent-specific and estimated gene-specific phenotypes between the pathogens B. abortus and S. typhimurium for Infectivity and the auxiliary phenotype of Viability. Unlike RSPs, GSPs exhibit biologically expected high correlation between (pathogen-independent) Viability phenotypes and only low to moderate correlation for Infectivity. b Gene set enrichment analysis: pathways significantly enriched at a false discovery rate (FDR) smaller than 0.25 for decreased Infectivity and gene lists from gespeR GSPs, haystack, RSA, and ISPs for all pathogens. Canonical pathway databases: R Reactome, K KEGG, ST Signal transduction KE. Pathways, such as focal adhesion or integrin- and TGF-β-signaling, shown to play a crucial role in pathogen entry, are enriched exclusively for GSPs; 62.5 % of pathways enriched for ISPs are also enriched for GSPs. RSA gene rankings are exclusively enriched for three pathways, while haystack rankings did not show sufficient overlap with any tested gene set (minimum overlap n = 15)

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