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Abstract：
Transcriptomic analysis across species is increasingly used to reveal conserved gene regulations which implicate crucial regulators. Cross-species analysis of single-cell RNA sequencing (scRNA-seq) data provides new opportunities to identify the cellular and molecular conservations, especially for cell types and cell type-specific gene regulations. However, few methods have been developed to analyze cross-species scRNA-seq data to uncover both molecular and cellular conservations. Here, we built a tool called CACIMAR, which can perform cross-species analysis of cell identities, markers, regulations, and interactions using scRNA-seq profiles. Based on the weighted sum models of the conserved features, we developed different conservation scores to measure the conservation of cell types, regulatory networks, and intercellular interactions. Using publicly available scRNA-seq data on retinal regeneration in mice, zebrafish, and chick, we demonstrated four main functions of CACIMAR. First, CACIMAR allows to identify conserved cell types even in evolutionarily distant species. Second, the tool facilitates the identification of evolutionarily conserved or species-specific marker genes. Third, CACIMAR enables the identification of conserved intracellular regulations, including cell type-specific regulatory subnetworks and regulators. Lastly, CACIMAR provides a unique feature for identifying conserved intercellular interactions. Overall, CACIMAR facilitates the identification of evolutionarily conserved cell types, marker genes, intracellular regulations, and intercellular interactions, providing insights into the cellular and molecular mechanisms of species evolution.
摘要：
跨物种的转录组学分析越来越多地用于揭示保守的基因调控，这些调控涉及关键的调控因子。单细胞RNA测序（scRNA-seq）数据的跨物种分析为识别细胞和分子保护提供了新的机会。特别是对于细胞类型和细胞类型特异性基因调控。然而,已经开发了很少的方法来分析跨物种scRNA-seq数据以揭示分子和细胞的保守。这里,我们建立了一个叫做CACIMAR的工具，可以进行细胞身份的跨物种分析，标记,法规,和使用scRNA-seq谱的相互作用。基于保守特征的加权和模型，我们开发了不同的保守分数来衡量细胞类型的保守性，监管网络,和细胞间的相互作用。使用公开可用的scRNA-seq数据对小鼠视网膜再生，斑马鱼,和小鸡，我们展示了CACIMAR的四个主要功能。首先,即使在进化上遥远的物种中，CACIMAR也可以识别保守的细胞类型。第二,该工具有助于鉴定进化保守或物种特异性标记基因。第三，CACIMAR能够识别保守的细胞内调节，包括细胞类型特定的监管子网络和监管机构。最后,CACIMAR提供了鉴定保守细胞间相互作用的独特特征。总的来说,CACIMAR促进了进化保守细胞类型的鉴定，标记基因，细胞内调节，和细胞间的相互作用，提供对物种进化的细胞和分子机制的见解。
