RT Journal Article
SR Electronic
T1 Alignment of time-course single-cell RNA-seq data with CAPITAL
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 859751
DO 10.1101/859751
A1 Reiichi Sugihara
A1 Yuki Kato
A1 Tomoya Mori
A1 Yukio Kawahara
YR 2019
UL http://biorxiv.org/content/early/2019/11/29/859751.abstract
AB Recent techniques on single-cell RNA sequencing have boosted transcriptome-wide observation of gene expression dynamics of time-course data at a single-cell scale. Typical examples of such analysis include inference of a pseudotime cell trajectory, and comparison of pseudotime trajectories between different experimental conditions will tell us how feature genes regulate a dynamic cellular process. Existing methods for comparing pseudotime trajectories, however, force users to select trajectories to be compared because they can deal only with simple linear trajectories, leading to the possibility of making a biased interpretation. Here we present CAPITAL, a method for comparing pseudotime trajectories with tree alignment whereby trajectories including branching can be compared without any knowledge of paths to be compared. Computational tests on time-series public data indicate that CAPITAL can align non-linear pseudotime trajectories and reveal gene expression dynamics.