美国密歇根大学Xiang Zhou研究小组开发了用于空间分辨转录组研究的空间表达模式统计分析方法。相关论文于2020年1月27日在线发表在《自然—方法学》杂志上。
Title: Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies
Author: Shiquan Sun, Jiaqiang Zhu, Xiang Zhou
Issue&Volume: 2020-01-27
Abstract: Identifying genes that display spatial expression patterns in spatially resolved transcriptomic studies is an important first step toward characterizing the spatial transcriptomic landscape of complex tissues. Here we present a statistical method, SPARK, for identifying spatial expression patterns of genes in data generated from various spatially resolved transcriptomic techniques. SPARK directly models spatial count data through generalized linear spatial models. It relies on recently developed statistical formulas for hypothesis testing, providing effective control of type I errors and yielding high statistical power. With a computationally efficient algorithm, which is based on penalized quasi-likelihood, SPARK is also scalable to datasets with tens of thousands of genes measured on tens of thousands of samples. Analyzing four published spatially resolved transcriptomic datasets using SPARK, we show it can be up to ten times more powerful than existing methods and disclose biological discoveries that otherwise cannot be revealed by existing approaches.
DOI: 10.1038/s41592-019-0701-7
Source: https://www.nature.com/articles/s41592-019-0701-7
Nature Methods:《自然—方法学》,创刊于2004年。隶属于施普林格·自然出版集团,最新IF:28.467
官方网址:https://www.nature.com/nmeth/
投稿链接:https://mts-nmeth.nature.com/cgi-bin/main.plex