Paper Info
Title
TimeCycle: topology inspired method for the detection of cycling transcripts in circadian time-series data
Abstract
Motivation: The circadian rhythm drives the oscillatory expression of thousands of genes across all tissues. The recent revolution in high-throughput transcriptomics, coupled with the significant implications of the circadian clock for human health, has sparked an interest in circadian profiling studies to discover genes under circadian control. Result: We present TimeCycle: a topology-based rhythm detection method designed to identify cycling transcripts. For a given time-series, the method reconstructs the state space using time-delay embedding, a data transformation technique from dynamical systems theory. In the embedded space, Takens' theorem proves that the dynamics of a rhythmic signal will exhibit circular patterns. The degree of circularity of the embedding is calculated as a persistence score using persistent homology, an algebraic method for discerning the topological features of data. By comparing the persistence scores to a bootstrapped null distribution, cycling genes are identified. Results in both synthetic and biological data highlight TimeCycle's ability to identify cycling genes across a range of sampling schemes, number of replicates and missing data. Comparison to competing methods highlights their relative strengths, providing guidance as to the optimal choice of cycling detection method.
Year
DOI
Venue
2021
10.1093/bioinformatics/btab476
BIOINFORMATICS
DocType
Volume
Issue
Conference
37
23
ISSN
Citations 
PageRank 
1367-4803
0
0.34
References 
Authors
0
2
Name
Order
Citations
PageRank
Elan Ness-Cohn100.34
Rosemary Braun278872.61