ChemGAPP: A tool for Chemical Genomics Analysis and Phenotypic Profiling

Hannah M Doherty, George Kritikos, Marco Galardini, Manuel Bazhaf, Danesh Moradigaravand

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: 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 ChemGAPP to bridge this gap. ChemGAPP integrates various steps in a streamlined and user-friendly format, including rigorous quality control measures to curate screening data. Results: ChemGAPP provides three sub-packages for different chemical-genomic screens: ChemGAPP Big for large-scale screens; ChemGAPP Small, for small-scale screens and ChemGAPP GI for genetic interaction screens. ChemGAPP Big, tested against the E. coli KEIO collection, revealed reliable fitness scores which displayed biologically relevant phenotypes. ChemGAPP Small, demonstrated significant changes in phenotype in a small-scale screen. ChemGAPP GI was benchmarked against three sets of genes with known epistasis types and successfully reproduced each interaction type.
Original languageEnglish (US)
JournalBioinformatics
DOIs
StatePublished - Apr 4 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-04-11
Acknowledged KAUST grant number(s): BAS/1/1108-01-01
Acknowledgements: HMD was funded by theWellcome Trust [222387/Z/21/Z]. MG was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy- EXC 2155- project number 390874280.MB was supported by a UKRI Future Leaders Fellowship [MR/V027204/1] and a Springboard award [SBF005\1112]. DM is a member of KAUST Smart-Health Initiative and funded by the baseline fund (BAS/1/1108-01-01).

ASJC Scopus subject areas

  • Biochemistry
  • Computational Theory and Mathematics
  • Computational Mathematics
  • Molecular Biology
  • Statistics and Probability
  • Computer Science Applications

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