ScGOclust: leveraging gene ontology to compare cell types across distant species using scRNA-seq data
ScGOclust: leveraging gene ontology to compare cell types across distant species using scRNA-seq data
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DOI：
10.1101/2024.01.09.574675
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发表时间：
2024-01
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影响因子：
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通讯作者：
Yuyao Song;Yanhui Hu;Julian A T Dow;Norbert Perrimon;I. Papatheodorou
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作者：
Yuyao Song;Yanhui Hu;Julian A T Dow;Norbert Perrimon;I. Papatheodorou
基本的生物过程在动物物种之间是共享的，但它们的细胞机制却截然不同。比较不同物种的细胞类型表达谱揭示了细胞功能的保守性和差异性。随着感兴趣物种之间系统发育距离的增加，基于基因的比较变得有限。基因本体（GO）知识库是最全面的基因功能资源，为比较遥远物种之间的细胞类型提供了桥梁。在这里，我们提出了 scGOclust，一种使用 GO 术语构建细胞功能图谱的计算工具，并促进物种内和物种间系统、稳健的比较。我们使用 scGOclust 来分析和比较小鼠和果蝇的心脏、肠道和肾脏。我们发现 scGOclust 概括了不同细胞类型的功能谱，表征了同源细胞类型之间的功能相似性，并揭示了不相关细胞类型之间的功能趋同。此外，我们通过 GO 配置文件的跨物种比较来识别果蝇中的亚群。最后，scGOclust 解决了马氏小管和肾段之间的类比问题。
Basic biological processes are shared among animal species, yet their cellular mechanisms are profoundly diverse. Comparing cell type expression profiles across species reveals the conservation and divergence of cellular functions. With the increase of phylogenetic distance between species of interest, a gene-based comparison becomes limited. The Gene Ontology (GO) knowledgebase is the most comprehensive resource of gene functions, providing a bridge for comparing cell types between remote species. Here, we present scGOclust, a computational tool to construct cellular functional profiles using GO terms and facilitates systematic, robust comparisons within and across species. We use scGOclust to analyse and compare the heart, gut and kidney between mouse and fly. We show that scGOclust recapitulates the function spectrum of different cell types, characterises functional similarities between homologous cell types, and reveals functional convergence between unrelated cell types. Furthermore, we identify subpopulations in the fly crop by cross-species comparison of GO profiles. Finally, scGOclust resolved the analogy between Malpighian tubule and kidney segments.