Discovering Biology in Periodic Data through Phase Set Enrichment Analysis (PSEA).

ABSTRACT: Several tools use prior biological knowledge to interpret gene expression data. However, existing enrichment tools assume that variables are monotonic and incorrectly measure the distance between periodic phases. As a result, these tools are poorly suited for the analysis of the cell cycle, circadian clock, or other periodic systems. Here, we develop Phase Set Enrichment Analysis (PSEA) to incorporate prior knowledge into the analysis of periodic data. PSEA identifies biologically related gene sets showing temporally coordinated expression. Using synthetic gene sets of various sizes generated from von Mises (circular normal) distributions, we benchmarked PSEA alongside existing methods. PSEA offered enhanced sensitivity over a broad range of von Mises distributions and gene set sizes. Impo

SUBMITTER: Zhang R 

PROVIDER: S-EPMC12931481 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature