ChemGAPP; A Package for Chemical Genomics Analysis and Phenotypic Profiling

Abstract

High-throughput chemical genomic screens produce informative datasets, providing valuable insights into unknown gene function on a genome-wide level. However, there is currently no comprehensive analytic package publicly available. We developed and benchmarked ChemGAPP to bridge this gap. ChemGAPP allows integration of various steps in a streamlined and user-friendly format, including rigorous quality control measures to curate screening data. ChemGAPP provides three sub-packages for different chemical-genomic screens: ChemGAPP Big for handling large-scale high-throughput screens; ChemGAPP Small, designed for small-scale screen analysis and ChemGAPP GI for genetic interaction screen analysis. ChemGAPP is available at https://github.com/HannahMDoherty/ChemGAPP.

Bam complex associated proteins inEscherichia coliare functionally linked to peptidoglycan biosynthesis, membrane fluidity and DNA replication

“…Endpoint pictures were taken to quantify colony fitness based on size by the image analysis software Iris (Kritikos et al, 2017). Fitness was scored using the chemical genomics analysis software ChemGAPP Small by comparing the mean colony size for the mutant in each condition to the mean colony size of that mutant in the LB agar condition, which was normalised to a fitness score of 1 (Doherty et al, 2023) This is unsurprising as SurA is the major chaperone pathway for OMPs to reach the Bam complex resulting in low fitness of DbamB and DsurA when growing on LB at 37°C. However, despite this functional link, they do not always phenocopy each other.…”

“…A total of 4 replica plates were generated for each stress condition. Fitness of the mutants was then scored and analysed using the ChemGAPP Small software (Doherty et al, 2023). Mean colony size for the mutant in each condition was compared to the mean colony size of that mutant in the LB agar condition, which was normalised to a fitness score of 1 (Doherty et al, 2023).…”

“…Fitness of the mutants was then scored and analysed using the ChemGAPP Small software (Doherty et al, 2023). Mean colony size for the mutant in each condition was compared to the mean colony size of that mutant in the LB agar condition, which was normalised to a fitness score of 1 (Doherty et al, 2023). Fitness scores below 1 represent decreased fitness, as a function of colony size compared to growth on LB agar, and scores above 1 indicate increased fitness in that condition.…”

“…Images were then analysed using the software called IRIS to measure the size, opacity and circularity of each colony on the plates (Kritikos et al, 2017). Fitness of the mutants was then analysed and compared using the software ChemGAPP GI (Doherty et al, 2023).…”