Oscope: A Statistical Approach for Identifying Oscillatory Genes in a Static RNA-Seq Experiment

• Activity Number: 418
• Type: Topic Contributed
• Date/Time: Tuesday, August 11, 2015 : 2:00 PM to 3:50 PM
• Sponsor: Scientific and Public Affairs Advisory Committee
• Author(s): Jeea Choi* and Shuyun Ye and Christina Kendziorski
• Companies: University of Wisconsin - Madison and University of Wisconsin - Madison and University of Wisconsin
• Keywords: Oscillatory ; RNA-seq ; expression ; frequency ; phase ; time-course RNA-seq

Abstract

Oscillatory gene expression is fundamental to mammalian development, homeostasis, and function; and disruptions in normal rhythms increase susceptibility to a number of diseases. Consequently, numerous biological and medical studies require the identification and characterization of oscillating genes. Toward this end, time-course RNA-seq experiments are the gold standard. However, these experiments are expensive and in some cases not possible. Oscope (Leng et al. 2015) was recently developed to identify oscillatory genes using data from a static RNA-seq experiment, and it has demonstrated utility in a number of areas. In short, Oscope identifies candidate oscillators, groups candidates having similar frequencies but perhaps varying phase, and then orders samples so that base cycles within each group can be reconstructed. In this work, we demonstrate the advantages and disadvantages of Oscope using simulated data as well as data from case studies. Improvements to each step in the pipeline are also detailed and evaluated.