Network analysis of gene essentiality in functional genomics experiments.
Network analysis of gene essentiality in functional genomics experiments.
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DOI：
10.1186/s13059-015-0808-9
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发表时间：
2015-10-30
期刊：
影响因子：
12.3
通讯作者：
Liu XS
中科院分区：
文献类型：
--
作者：
Jiang P;Wang H;Li W;Zang C;Li B;Wong YJ;Meyer C;Liu JS;Aster JC;Liu XS
已经开发了许多基因组技术来研究基因组范围内的基因必要性，例如CRISPR和shRNA筛选。我们对公共CRISPR筛选的分析表明，当与基因表达或组蛋白标记整合时，蛋白质相互作用网络对基因的重要性具有高度预测性。同时，通过网络邻居信息可以显著提高CRISPR和shRNA筛选结果的质量。我们还发现网络邻居信息在优先考虑ChIP-seq靶基因和肿瘤分析中的生存指标基因方面非常有用。因此，我们的研究提供了一个通用的方法，基因的必要性分析的功能基因组实验（http：nest.dfci.harvard.edu）。本文的在线版本（doi：10.1186/s13059-015-0808-9）包含补充材料，可供授权用户使用。
Many genomic techniques have been developed to study gene essentiality genome-wide, such as CRISPR and shRNA screens. Our analyses of public CRISPR screens suggest protein interaction networks, when integrated with gene expression or histone marks, are highly predictive of gene essentiality. Meanwhile, the quality of CRISPR and shRNA screen results can be significantly enhanced through network neighbor information. We also found network neighbor information to be very informative on prioritizing ChIP-seq target genes and survival indicator genes from tumor profiling. Thus, our study provides a general method for gene essentiality analysis in functional genomic experiments (http://nest.dfci.harvard.edu). The online version of this article (doi:10.1186/s13059-015-0808-9) contains supplementary material, which is available to authorized users.