ChemGAPP: A tool for Chemical Genomics Analysis and Phenotypic Profiling

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

doi:10.1093/bioinformatics/btad171

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 journal › Article › peer-review

3 Scopus citations

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 language	English (US)
Journal	Bioinformatics
DOIs	https://doi.org/10.1093/bioinformatics/btad171
State	Published - 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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10.1093/bioinformatics/btad171

https://repository.kaust.edu.sa/bitstream/10754/687395/6/btad171.pdf

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title = "ChemGAPP: A tool for Chemical Genomics Analysis and Phenotypic Profiling",

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.",

author = "Doherty, {Hannah M} and George Kritikos and Marco Galardini and Manuel Bazhaf and Danesh Moradigaravand",

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).",

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AU - Doherty, Hannah M

AU - Kritikos, George

AU - Galardini, Marco

AU - Bazhaf, Manuel

AU - Moradigaravand, Danesh

N1 - 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).

PY - 2023/4/4

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N2 - 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.

AB - 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.

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ChemGAPP: A tool for Chemical Genomics Analysis and Phenotypic Profiling

Abstract

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