A set-theoretic definition of cell types with an algebraic structure on gene regulatory networks and application in annotation of RNA-seq data

Yuji Okano, Yoshitaka Kase, Hideyuki Okano

研究成果: ジャーナルへの寄稿学術論文査読

抄録

The emergence of single-cell RNA sequencing (RNA-seq) has radically changed the observation of cellular diversity. Although annotations of RNA-seq data require preserved properties among cells of an identity, annotations using conventional methods have not been able to capture universal characters of a cell type. Analysis of expression levels cannot be accurately annotated for cells because differences in transcription do not necessarily explain biological characteristics in terms of cellular functions and because the data themselves do not inform about the correct mapping between cell types and genes. Hence, in this study, we developed a new representation of cellular identities that can be compared over different datasets while preserving nontrivial biological semantics. To generalize the notion of cell types, we developed a new framework to manage cellular identities in terms of set theory. We provided further insights into cells by installing mathematical descriptions of cell biology. We also performed experiments that could correspond to practical applications in annotations of RNA-seq data.

本文言語英語
ページ(範囲)113-130
ページ数18
ジャーナルStem Cell Reports
18
1
DOI
出版ステータス出版済み - 10-01-2023
外部発表はい

All Science Journal Classification (ASJC) codes

  • 生化学
  • 遺伝学
  • 発生生物学
  • 細胞生物学

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