TIMER2.0 for analysis of tumor-infiltrating immune cells
Taiwen Li1, Jingxin Fu2,3, Zexian Zeng2
1State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China.
Nucleic Acids Research
|May 23, 2020
Summary
TIMER2.0 enhances tumor immune infiltration analysis using six algorithms for robust estimation. This web platform aids in understanding tumor-immune interactions and their associations with clinical and genomic features across multiple cancers.
Area of Science:
- Immunology
- Bioinformatics
- Computational Biology
Background:
- Tumor microenvironment immune cell composition impacts cancer progression and immunotherapy.
- Computational algorithms infer immune infiltrates from transcriptome data, linking them to genomic changes.
- Analyzing these interactions in large public datasets presents challenges.
Purpose of the Study:
- To improve analysis of tumor-immune interactions by enhancing the TIMER web platform.
- To provide robust estimation of immune infiltration levels using multiple algorithms.
- To facilitate exploration of associations between immune infiltrates and tumor characteristics.
Main Methods:
- Developed TIMER2.0, an upgraded web platform utilizing six state-of-the-art algorithms for immune infiltration estimation.
- Integrated The Cancer Genome Atlas (TCGA) data and user-provided tumor profiles.
- Implemented four modules for genetic/clinical associations and four for TCGA cohort exploration.
Main Results:
- TIMER2.0 offers more robust immune infiltration level estimations compared to single-algorithm methods.
- The platform enables comprehensive analysis and visualization of tumor-infiltrating immune cells.
- Functional heatmap tables allow simultaneous identification of significant associations across multiple cancer types.
Conclusions:
- TIMER2.0 lowers barriers for analyzing complex tumor-immune interactions in large public datasets.
- The enhanced platform provides valuable insights into the interplay between tumor genetics, clinical features, and immune infiltrates.
- TIMER2.0 serves as a comprehensive resource for researchers studying tumor immunology and cancer genomics.
