1. scEGOT: single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport
- Author
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Toshiaki Yachimura, Hanbo Wang, Yusuke Imoto, Momoko Yoshida, Sohei Tasaki, Yoji Kojima, Yukihiro Yabuta, Mitinori Saitou, and Yasuaki Hiraoka
- Subjects
Trajectory inference ,Optimal transport ,Gaussian mixture model ,Single-cell biology ,Epigenetic landscape ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Time-series scRNA-seq data have opened a door to elucidate cell differentiation, and in this context, the optimal transport theory has been attracting much attention. However, there remain critical issues in interpretability and computational cost. Results We present scEGOT, a comprehensive framework for single-cell trajectory inference, as a generative model with high interpretability and low computational cost. Applied to the human primordial germ cell-like cell (PGCLC) induction system, scEGOT identified the PGCLC progenitor population and bifurcation time of segregation. Our analysis shows TFAP2A is insufficient for identifying PGCLC progenitors, requiring NKX1-2. Additionally, MESP1 and GATA6 are also crucial for PGCLC/somatic cell segregation. Conclusions These findings shed light on the mechanism that segregates PGCLC from somatic lineages. Notably, not limited to scRNA-seq, scEGOT’s versatility can extend to general single-cell data like scATAC-seq, and hence has the potential to revolutionize our understanding of such datasets and, thereby also, developmental biology.
- Published
- 2024
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