TIMER3: an enhanced resource for tumor immune analysis.

Abstract

The tumor immune microenvironment plays a critical role in tumor progression and immunotherapy response, with the abundance and composition of infiltrating immune cells serving as key determinants of therapeutic outcomes. Given the limitations of direct experimental methods, computational deconvolution algorithms are widely applied to infer immune cell infiltration from bulk RNA-seq data. While such estimates have proven valuable for studying tumor-immune interactions, large-scale, systematic analyses across multiple cancer types and treatment contexts remain limited. To address this need, we developed TIMER3 (https://compbio.cn/timer3/), an upgraded web server that substantially extends the functionality and scope of its predecessors. TIMER3 integrates 15 state-of-the-art immune deconvolution algorithms, including both human-specific and mouse-specific methods, to improve the robustness and interpretability of immune cell estimation. It incorporates an expanded collection of public RNA-seq datasets of immunotherapy-related cohorts, enabling large-scale analyses of immune dynamics across pre-treatment and post-treatment conditions. TIMER3 introduces new analytical modules for immunotherapy response, signature-based functional profiling, and interactive visualization of cell composition, gene expression, and survival associations. Collectively, TIMER3 provides a comprehensive, user-friendly platform for dissecting the TIME across diverse datasets, facilitating translational research and precision immuno-oncology.