High-dimensional omics data analysis using a variable screening protocol with prior knowledge integration (SKI). Issue 4 (December 2016)

• Record Type: Journal Article
• Authors: Liu, Cong; Jiang, Jianping; Gu, Jianlei; Yu, Zhangsheng; Wang, Tao; Lu, Hui
• Is Part Of: BMC systems biology. Volume 10:Issue 4(2016)
• Page Start: 457
• Page End: 464
• Publication Date: 2016-12
• Subjects: Variable selection -- Dimension reduction -- Sure independence screening -- Knowledge integration -- SKI; Biological systems -- Periodicals; Biology -- Research -- Periodicals; Cell physiology -- Periodicals; Genes -- Analysis -- Periodicals; 571
• DOI: 10.1186/s12918-016-0358-0
• Languages: English
• ISSNs: 1752-0509

Abstract

Abstract Background High-throughput technology could generate thousands to millions biomarker measurements in one experiment. However, results from high throughput analysis are often barely reproducible due to small sample size. Different statistical methods have been proposed to tackle this "small n and large p" scenario, for example different datasets could be pooled or integrated together to provide an effective way to improve reproducibility. However, the raw data is either unavailable or hard to integrate due to different experimental conditions, thus there is an emerging need to develop a method for "knowledge integration" in high-throughput data analysis. Results In this study, we proposed an integrative prescreening approach, SKI, for high-throughput data analysis. A new rank is generated based on two initial ranks: (1) knowledge based rank; and (2) marginal correlation based rank. Our simulation shows the SKI outperforms other methods without knowledge-integration in terms of higher true positive rate given the same number of variables selected. We also applied our method in a drug response study and found its performance to be better than regular screening methods. Conclusion The proposed method provides an effective way to integrate knowledge for high-throughput analysis. It could easily implemented with our provided R package named SKI.