ChemGAPP：用于化学基因组学分析和表型分析的工具。

ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling.

机构信息

Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany.

出版信息

Bioinformatics. 2023 Apr 3;39(4). doi: 10.1093/bioinformatics/btad171.

DOI:10.1093/bioinformatics/btad171

PMID:37014365

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10085634/

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 Escherichiacoli 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.

AVAILABILITY AND IMPLEMENTATION

ChemGAPP is available at https://github.com/HannahMDoherty/ChemGAPP, as a standalone Python package as well as Streamlit applications.

摘要

动机

高通量化学基因组筛选产生了有信息量的数据集，为全面了解基因组水平上未知基因功能提供了有价值的见解。然而，目前还没有公开的综合分析软件包。我们开发了 ChemGAPP 来弥补这一空白。ChemGAPP 以精简和用户友好的格式集成了各个步骤，包括严格的质量控制措施来管理筛选数据。

结果

ChemGAPP 为不同的化学基因组筛选提供了三个子包：ChemGAPP Big 用于大规模筛选；ChemGAPP Small 用于小规模筛选；以及 ChemGAPP GI 用于遗传相互作用筛选。ChemGAPP Big 在大肠杆菌 KEIO 集合上进行了测试，结果显示可靠的适合度分数，显示出具有生物学相关性的表型。ChemGAPP Small 在小规模筛选中显示出显著的表型变化。ChemGAPP GI 与三组具有已知上位类型的基因进行了基准测试，并成功再现了每种相互作用类型。