Assessing consistency across functional screening datasets in cancer cells.
Assessing consistency across functional screening datasets in cancer cells.
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DOI：
10.1093/bioinformatics/btab423
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发表时间：
2021-12-07
期刊：
影响因子：
--
通讯作者：
Xie Y
中科院分区：
文献类型：
--
作者：
Cai L;Liu H;Minna JD;DeBerardinis RJ;Xiao G;Xie Y
许多高通量筛选研究已经在癌细胞系中进行，以确定治疗药物和靶点。现有的一致性评估研究一次只检查两个数据集，结论基于精心选择的特征子集，而不是考虑所有数据的全局一致性。然而，即使选择的特征高度一致，仍然可以观察到大部分数据的一致性差。在这项研究中，我们收集了9个化合物筛选数据集和3个功能基因组学数据集。我们基于功能数据和拷贝数调整后的基因表达数据之间的关联，推导出一致性的直接度量以及一致性的间接度量。这些结果已经集成到一个web应用程序中——功能数据一致性浏览器（FDCE），允许用户进行查询和生成交互式可视化，以便可以评估感兴趣的单个特征的功能数据一致性。我们开发的FDCE网络工具和我们生成的功能数据一致性度量可以在https://lccl.shinyapps.io/FDCE/上获得。补充数据可在生物信息学网站获得。
Many high-throughput screening studies have been carried out in cancer cell lines to identify therapeutic agents and targets. Existing consistency assessment studies only examined two datasets at a time, with conclusions based on a subset of carefully selected features rather than considering global consistency of all the data. However, poor concordance can still be observed for a large part of the data even when selected features are highly consistent. In this study, we assembled nine compound screening datasets and three functional genomics datasets. We derived direct measures of consistency as well as indirect measures of consistency based on association between functional data and copy number-adjusted gene expression data. These results have been integrated into a web application—the Functional Data Consistency Explorer (FDCE), to allow users to make queries and generate interactive visualizations so that functional data consistency can be assessed for individual features of interest. The FDCE web tool and we have developed and the functional data consistency measures we have generated are available at https://lccl.shinyapps.io/FDCE/. Supplementary data are available at Bioinformatics online.
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影响因子：
64.5
作者：
Basu A;Bodycombe NE;Cheah JH;Price EV;Liu K;Schaefer GI;Ebright RY;Stewart ML;Ito D;Wang S;Bracha AL;Liefeld T;Wawer M;Gilbert JC;Wilson AJ;Stransky N;Kryukov GV;Dancik V;Barretina J;Garraway LA;Hon CS;Munoz B;Bittker JA;Stockwell BR;Khabele D;Stern AM;Clemons PA;Shamji AF;Schreiber SL
通讯作者：
Schreiber SL
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14.9
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Kim S;Thiessen PA;Bolton EE;Chen J;Fu G;Gindulyte A;Han L;He J;He S;Shoemaker BA;Wang J;Yu B;Zhang J;Bryant SH
通讯作者：
Bryant SH
影响因子：
11.2
作者：
Hatzis C;Bedard PL;Birkbak NJ;Beck AH;Aerts HJ;Stem DF;Shi L;Clarke R;Quackenbush J;Haibe-Kains B
通讯作者：
Haibe-Kains B
影响因子：
10.3
作者：
Polley, Eric;Kunkel, Mark;Teicher, Beverly A.
通讯作者：
Teicher, Beverly A.
影响因子：
64.8
作者：
Ghandi, Mahmoud;Huang, Franklin W.;Sellers, William R.
通讯作者：
Sellers, William R.