PDF(Pubmed)
Abstract：
Recent advances in CRISPR-Cas9 engineering and single-cell assays have enabled the simultaneous measurement of single-cell transcriptomic and phylogenetic profiles. However, there are few computational tools enabling users to integrate and derive insight from a joint analysis of these two modalities. Here, we describe \"PhyloVision\": an open-source software for interactively exploring data from both modalities and for identifying and interpreting heritable gene modules whose concerted expression are associated with phylogenetic relationships. PhyloVision provides a feature-rich, interactive, and shareable web-based report for investigating these modules while also supporting several other data and meta-data exploration capabilities. We demonstrate the utility of PhyloVision using a published dataset of metastatic lung adenocarcinoma cells, whose phylogeny was resolved using a CRISPR-Cas9-based lineage-tracing system. Together, we anticipate that PhyloVision and the methods it implements will be a useful resource for scalable and intuitive data exploration for any assay that simultaneously measures cell state and lineage.
摘要：
CRISPR-Cas9工程和单细胞测定的最新进展使得能够同时测量单细胞转录组和系统发育谱。然而,很少有计算工具使用户能够从这两种模式的联合分析中整合和获得洞察力。这里,我们描述了“PhyloVision”：一种开源软件，用于交互式地探索来自两种模式的数据，并用于识别和解释其协同表达与系统发育关系相关的可遗传基因模块。PhyloVision提供了一个功能丰富的,互动式,和可共享的基于Web的报告，用于调查这些模块，同时还支持其他一些数据和元数据探索功能。我们使用已发表的转移性肺腺癌细胞数据集证明了PhyloVision的实用性，使用基于CRISPR-Cas9的谱系追踪系统解析了其系统发育。一起,我们预计，PhyloVision及其实现的方法将是一个有用的资源，用于可扩展和直观的数据探索，用于任何同时测量细胞状态和谱系的测定。
