相似性(几何)
成对比较
计算机科学
转录组
概率逻辑
模式识别(心理学)
计算生物学
数据挖掘
人工智能
生物
基因
图像(数学)
基因表达
遗传学
作者
Ron Zeira,Max Land,Alexander Strzalkowski,Benjamin J. Raphael
出处
期刊:Nature Methods
[Springer Nature]
日期:2022-05-01
卷期号:19 (5): 567-575
被引量:73
标识
DOI:10.1038/s41592-022-01459-6
摘要
Spatial transcriptomics (ST) measures mRNA expression across thousands of spots from a tissue slice while recording the two-dimensional (2D) coordinates of each spot. We introduce probabilistic alignment of ST experiments (PASTE), a method to align and integrate ST data from multiple adjacent tissue slices. PASTE computes pairwise alignments of slices using an optimal transport formulation that models both transcriptional similarity and physical distances between spots. PASTE further combines pairwise alignments to construct a stacked 3D alignment of a tissue. Alternatively, PASTE can integrate multiple ST slices into a single consensus slice. We show that PASTE accurately aligns spots across adjacent slices in both simulated and real ST data, demonstrating the advantages of using both transcriptional similarity and spatial information. We further show that the PASTE integrated slice improves the identification of cell types and differentially expressed genes compared with existing approaches that either analyze single ST slices or ignore spatial information.
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