PGS: A tool for association study of high-dimensional microRNA expression data with repeated measures

Yinan Zheng, Zhe Fei, Wei Zhang, Justin B. Starren, Lei Liu, Andrea A. Baccarelli, Yi Li, Lifang Hou*

*Corresponding author for this work

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

Motivation: MicroRNAs (miRNAs) are short single-stranded non-coding molecules that usually function as negative regulators to silence or suppress gene expression. Owning to the dynamic nature of miRNA and reduced microarray and sequencing costs, a growing number of researchers are now measuring high-dimensional miRNA expression data using repeated or multiple measures in which each individual has more than one sample collected and measured over time. However, the commonly used univariate association testing or the site-by-site (SBS) testing may underutilize the longitudinal feature of the data, leading to underpowered results and less biologically meaningful results. Results: We propose a penalized regression model incorporating grid search method (PGS), for analyzing associations of high-dimensional miRNA expression data with repeated measures. The development of this analytical framework was motivated by a real-world miRNA dataset. Comparisons between PGS and the SBS testing revealed that PGS provided smaller phenotype prediction errors and higher enrichment of phenotype-related biological pathways than the SBS testing. Our extensive simulations showed that PGS provided more accurate estimates and higher sensitivity than the SBS testing with comparable specificities.

Original languageEnglish (US)
Pages (from-to)2802-2807
Number of pages6
JournalBioinformatics
Volume30
Issue number19
DOIs
StatePublished - Apr 2 2014

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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