Kannan Lavanya, Ramos Marcel, Re Angela, El-Hachem Nehme, Safikhani Zhaleh, Gendoo Deena M A, Davis Sean, Gomez-Cabrero David, Castelo Robert, Hansen Kasper D, Carey Vincent J, Morgan Martin, Culhane Aedín C, Haibe-Kains Benjamin, Waldron Levi
Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12.
Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.
通过DNA测序、RNA和微小RNA分析、蛋白质组学及其他检测手段对生物样本进行分子层面的探究，有可能提供一种系统层面的方法来预测治疗反应和疾病进展，并开发精准疗法。大型公共资助项目已生成了广泛且可免费获取的多检测数据资源；然而，用于分析此类实验的生物信息学和统计方法仍处于起步阶段。我们综述了临床肿瘤学、药物基因组学及其他扰动实验、群体基因组学和调控基因组学等领域的多检测基因组数据资源以及数据采集工具。最后，我们综述了专门用于整合基因组数据可视化和分析的生物信息学工具。本综述为获取公开可用的数据和工具提供了起点，以支持所需整合方法的开发。
