A comprehensive comparison on cell-type composition inference for spatial transcriptomics data

反褶积 背景(考古学) 推论 计算机科学 表达式(计算机科学) 计算生物学 转录组 数据挖掘 模式识别(心理学)
作者
Jiawen Chen,Weifang Liu,Tianyou Luo,Zhentao Yu,Minzhi Jiang,Jia Wen,Gaorav P Gupta,Paola Giusti,Hongtu Zhu,Yuchen Yang,Yun Li
出处
期刊:Briefings in Bioinformatics [Oxford University Press]
标识
DOI:10.1093/bib/bbac245
摘要

Abstract Spatial transcriptomics (ST) technologies allow researchers to examine transcriptional profiles along with maintained positional information. Such spatially resolved transcriptional characterization of intact tissue samples provides an integrated view of gene expression in its natural spatial and functional context. However, high-throughput sequencing-based ST technologies cannot yet reach single cell resolution. Thus, similar to bulk RNA-seq data, gene expression data at ST spot-level reflect transcriptional profiles of multiple cells and entail the inference of cell-type composition within each ST spot for valid and powerful subsequent analyses. Realizing the critical importance of cell-type decomposition, multiple groups have developed ST deconvolution methods. The aim of this work is to review state-of-the-art methods for ST deconvolution, comparing their strengths and weaknesses. In particular, we construct ST spots from single-cell level ST data to assess the performance of 10 methods, with either ideal reference or non-ideal reference. Furthermore, we examine the performance of these methods on spot- and bead-level ST data by comparing estimated cell-type proportions to carefully matched single-cell ST data. In comparing the performance on various tissues and technological platforms, we concluded that RCTD and stereoscope achieve more robust and accurate inferences.
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