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TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq
Mengyu Xie1, Kyubum Lee1, John H Lockhart2
1Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
Bioinformatics (Oxford, England)
|April 26, 2021
Summary
We developed TIMEx, a new method to analyze immune cells in tumors using bulk transcriptomics. This tool helps understand cancer progression and treatment response by examining the tumor-immune microenvironment (TIME).
Area of Science:
- Cancer Biology
- Immunology
- Bioinformatics
Background:
- The tumor-immune microenvironment (TIME) is crucial for cancer progression, metastasis, and treatment efficacy.
- Understanding the cellular composition of the TIME is essential for developing targeted therapies.
Purpose of the Study:
- To introduce TIMEx, a novel deconvolution method for estimating infiltrating immune cells in bulk transcriptomics data.
- To provide a user-friendly web portal for evaluating TIMEx and comparing it with other deconvolution methods.
Main Methods:
- TIMEx utilizes pan-cancer single-cell RNA-seq signatures to deconvolute bulk transcriptomic profiles.
- The method specifically emphasizes the estimation of infiltrating immune cells within the TIME.
Main Results:
- TIMEx enables a more accurate assessment of immune cell infiltration from bulk RNA sequencing data.
- The developed web portal allows researchers to easily apply and compare deconvolution methods.
Conclusions:
- TIMEx is a valuable new tool for analyzing the tumor-immune microenvironment.
- The TIMEx web portal facilitates the evaluation and application of TIME deconvolution methods in cancer research.
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