Jain Yashita, Ding Shanshan, Qiu Jing
Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
Department of Applied Economics and Statistics, University of Delaware, 531 S College Ave., Newark, DE 19711, USA.
Stat Appl Genet Mol Biol. 2019 Jan 26;18(1):/j/sagmb.2019.18.issue-1/sagmb-2018-0028/sagmb-2018-0028.xml. doi: 10.1515/sagmb-2018-0028.
Advancement in next-generation sequencing, transcriptomics, proteomics and other high-throughput technologies has enabled simultaneous measurement of multiple types of genomic data for cancer samples. These data together may reveal new biological insights as compared to analyzing one single genome type data. This study proposes a novel use of supervised dimension reduction method, called sliced inverse regression, to multi-omics data analysis to improve prediction over a single data type analysis. The study further proposes an integrative sliced inverse regression method (integrative SIR) for simultaneous analysis of multiple omics data types of cancer samples, including MiRNA, MRNA and proteomics, to achieve integrative dimension reduction and to further improve prediction performance. Numerical results show that integrative analysis of multi-omics data is beneficial as compared to single data source analysis, and more importantly, that supervised dimension reduction methods possess advantages in integrative data analysis in terms of classification and prediction as compared to unsupervised dimension reduction methods.
下一代测序、转录组学、蛋白质组学和其他高通量技术的进步,使得能够同时测量癌症样本的多种类型基因组数据。与分析单一类型的基因组数据相比,这些数据共同揭示了新的生物学见解。本研究提出了一种监督降维方法——切片逆回归在多组学数据分析中的新应用,以改善单一数据类型分析的预测效果。该研究进一步提出了一种整合切片逆回归方法(integrative SIR),用于同时分析癌症样本的多种组学数据类型,包括miRNA、mRNA和蛋白质组学,以实现整合降维并进一步提高预测性能。数值结果表明,与单一数据源分析相比,多组学数据的整合分析是有益的,更重要的是,与无监督降维方法相比,监督降维方法在整合数据分析的分类和预测方面具有优势。
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