Protocol to detect immune levels, abnormal metabolism, and signaling pathways in tumor tissue based on scRNA-seq obtained from patient databases

Weiyu Bai

doi:10.1016/j.xpro.2024.103065

Protocol to detect immune levels, abnormal metabolism, and signaling pathways in tumor tissue based on scRNA-seq obtained from patient databases

STAR Protoc. 2024 May 14;5(2):103065. doi: 10.1016/j.xpro.2024.103065. Online ahead of print.

Author

Weiyu Bai¹

Affiliation

¹ Center for Life Sciences, School of Life Sciences, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China. Electronic address: 925605397@qq.com.

Abstract

Malignant tumor cells are typically more active in terms of metabolism and signal transduction compared to immune and normal cells. Here, we present a protocol to evaluate immune levels, abnormal metabolism, and signaling pathways in tumor tissue based on single-cell sequencing based on patient data obtained from the GEO database. We describe steps for tumor immune microenvironment (TIME)-based evaluation, tumor purity assessment, and identification of abnormal signal transduction and metabolic pathways. We then detail procedures for screening hub genes. For complete details on the use and execution of this protocol, please refer to Bai et al.¹.

Keywords: Bioinformatics; Cancer; Sequence analysis.