TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.
TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.
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DOI：
10.1093/nar/gkv1507
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发表时间：
2016-05-05
影响因子：
14.9
通讯作者：
Noushmehr H
中科院分区：
文献类型：
--
作者：
Colaprico A;Silva TC;Olsen C;Garofano L;Cava C;Garolini D;Sabedot TS;Malta TM;Pagnotta SM;Castiglioni I;Ceccarelli M;Bontempi G;Noushmehr H
癌症基因组图谱（TCGA）研究网络已经公开了33种不同肿瘤类型的10000多名肿瘤患者的临床和分子表型的大量集合。使用这个队列，TCGA已经发表了20多篇标记论文，详细描述了与这些肿瘤类型相关的基因组和表观基因组改变。尽管TCGA的研究网络已经取得了许多重要的发现，但仍然存在实施新方法的机会，从而阐明新的生物学途径和诊断标志物。然而，挖掘TCGA数据提出了一些生物信息学挑战，例如数据检索以及与临床数据和其他分子数据类型（例如RNA和DNA甲基化）的整合。我们开发了一个R/Bioconductor软件包，称为TCGAbiolinks，以解决这些挑战，并通过使用指导工作流程提供生物信息学解决方案，允许用户查询，下载和执行TCGA数据的综合分析。我们将计算机科学和统计学的方法结合到管道中，并将以前的TCGA标记物研究和我们自己的小组中开发的方法纳入其中。使用四种不同的TCGA肿瘤类型（肾，脑，乳腺和结肠）为例，我们提供了案例研究，以说明不同Bioconductor包的可重复性，综合分析和利用的例子，以推进和加速新的发现。
The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries.