TimiGP: An R Package to Depict the Tumor Microenvironment from Bulk Transcriptomics

Authors

Chenyang Li
Jianjun Zhang
Chao Cheng

Publication Date

12-15-2023

Journal

STAR Protocols

DOI

10.1016/j.xpro.2023.102742

PMID

38019649

PMCID

PMC10698325

PubMedCentral® Posted Date

11-27-2023

PubMedCentral® Full Text Version

Post-Print

Published Open-Access

yes

Keywords

Humans, Tumor Microenvironment, Gene Expression Profiling, Cell Communication, Neoplasms, Bioinformatics, Single Cell, Cancer, Genomics, RNA-seq, Immunology, Gene Expression, Systems biology

Abstract

Exploring the clinical relevance of diverse immune cell types within the tumor microenvironment is pivotal for unraveling cancer intricacies and developing treatments. Here, we present a protocol for using tumor immune microenvironment illustration based on gene pairs, an R package to deduce cell-cell interactions, unveiling the association between immune cell relative abundance and patient prognoses from bulk gene expression and survival data. We describe steps for harnessing cell-type markers derived from single-cell RNA sequencing data to map the tumor immune microenvironment across a spectrum of cancer types. For complete details on the use and execution of this protocol, please refer to Li et al. (2023).

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