論文 - 詳細
| RRC ID | 89295 |
|---|---|
| 著者 | Yuya Tokuta, Tomonori Nakamura, Kohei Fujiwara, Masanori Imamura, Masahiro Nagano, Mitinori Saitou, Yusuke Imoto, Yasuaki Hiraoka |
| タイトル | Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport |
| Abstract |
Sequence homology reveals evolutionary gene correspondences, but identifying functionally corresponding genes within specific cell types or during cell fate specification remains non-trivial. Here, frameworks that translate insights from model organisms into other species would accelerate wet-lab studies, so we develop Species-OT, a cross-species transcriptome analysis framework using Gromov-Wasserstein optimal transport, which quantitatively compares the geometry of transcriptome distributions. Given a pair of bulk or single-cell RNA-sequencing datasets, Species-OT returns a gene-to-gene correspondence capturing probabilistic alignments of regulatory roles, and a transcriptomic distance quantifying overall divergence. Applied pairwise, Species-OT yields a transcriptomic discrepancy array and a hierarchical clustering tree analogous to a phylogenetic tree. We validate Species-OT using bulk RNA-seq data for cell fate specification from pluripotent stem cells in mice, monkeys, and humans and scRNA-seq data from pluripotent stem cells of six mammalian species. Species-OT identifies gene correspondences within cell fate specification, while transcriptomic discrepancies recapitulate expected species relationships. |
| 公開日 | 2025-10-24 |
| DOI | 10.1101/2025.10.23.684069 |
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