ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling.
ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling.
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DOI：
10.1093/bioinformatics/btad171
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发表时间：
2023-04-03
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影响因子：
--
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高通量化学基因组筛选产生信息丰富的数据集，在全基因组水平上提供对未知基因功能的有价值的见解。然而，目前还没有公开可用的全面分析包。我们开发了ChemGAPP来弥合这一差距。ChemGAPP以简化和用户友好的格式集成了各种步骤，包括严格的质量控制措施来精选筛查数据。ChemGAPP为不同的化学基因组筛选提供了三个子包：用于大规模筛选的ChemGAPP Big；用于小规模筛选的ChemGAPP Small；以及用于遗传交互筛选的ChemGAPP GI。ChemGAPP Big与Escherichiacoli Keio系列进行了测试，显示了可靠的健康评分，显示了生物相关的表型。ChemGAPP Small在小范围筛选中表现出明显的表型变化。ChemGAPP GI以三组已知上位性类型的基因为基准，并成功地复制了每一种交互类型。ChemGAPP可以在https://github.com/HannahMDoherty/ChemGAPP，上以独立的Python包和Streamlight应用程序的形式获得。
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. 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. ChemGAPP is available at https://github.com/HannahMDoherty/ChemGAPP, as a standalone Python package as well as Streamlit applications.
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DOI：
10.1073/pnas.0712255105
发表时间：
2008-03-04
影响因子：
11.1
作者：
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通讯作者：
Roth, Frederick P.
影响因子：
64.8
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影响因子：
9.9
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影响因子：
48
作者：
Baryshnikova, Anastasia;Costanzo, Michael;Kim, Yungil;Ding, Huiming;Koh, Judice;Toufighi, Kiana;Youn, Ji-Young;Ou, Jiongwen;San Luis, Bryan-Joseph;Bandyopadhyay, Sunayan;Hibbs, Matthew;Hess, David;Gingras, Anne-Claude;Bader, Gary D.;Troyanskaya, Olga G.;Brown, Grant W.;Andrews, Brenda;Boone, Charles;Myers, Chad L.
通讯作者：
Myers, Chad L.
影响因子：
3.7
作者：
Fajardo A;Martínez-Martín N;Mercadillo M;Galán JC;Ghysels B;Matthijs S;Cornelis P;Wiehlmann L;Tümmler B;Baquero F;Martínez JL
通讯作者：
Martínez JL