ChemGAPP

ChemGAPP analyzes high-throughput chemical genomic screens to compute fitness scores and detect phenotypic changes and genetic interactions.

Key Features:

• Quality control: Implements rigorous quality control measures for curation of screening data.
• Fitness scoring: Computes reliable fitness scores that correspond to biologically relevant phenotypes.
• ChemGAPP Big: Tailored for large-scale screens and tested using the Escherichia coli KEIO collection to generate reliable fitness scores.
• ChemGAPP Small: Optimized for small-scale screens and for detecting significant changes in phenotype.
• ChemGAPP GI (Genetic Interaction): Developed for genetic interaction screens and benchmarked against three sets of genes with known epistasis types, reproducing each interaction type.

Scientific Applications:

• Genome-wide gene function inference: Enables inference of gene function from chemical perturbation fitness profiles.
• Phenotypic profiling: Profiles mutant phenotypes in response to chemical treatments.
• Genetic interaction mapping: Identifies and characterizes genetic interactions and epistasis types.
• Benchmarking and validation: Supports validation of analytical results using the Escherichia coli KEIO collection and gene sets with known epistasis.

Methodology:

Performs rigorous quality control on screening data, computes fitness scores, detects significant phenotypic changes, and benchmarks genetic interactions against three sets of genes with known epistasis types.