ArticleNucleic acids research2025
TIMER3: an enhanced resource for tumor immune analysis.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers, 1 of them a synthesis that pooled it.
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Who cites it
74 citing papers in PubMed, 1 synthesis or guideline pooled it.
- RGS Family Remodeling in Breast Cancer: A Meta-Analysis and Multi-Omics Profiling of Prognostic Biomarkers.Cancer medicine · 2026Pooled it
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- Big Data and Artificial Intelligence in Cancer Drug Discovery: Promise, Challenges, and Emerging Opportunities.Cancers · 2026Review
- NF1 loss in estrogen receptor-positive breast cancer induces osteoclast formation and immunosuppression to promote bone metastasis.Cancer letters · 2026Article
- Article
- Exploratory Multi-Platform Bioinformatic Analysis of MEAK7 and Its Molecular, Survival, and Immune Associations in Pancreatic Ductal Adenocarcinoma.International journal of molecular sciences · 2026Article
- Immune-associated alternative splicing signatures define molecular subtypes in breast cancer.iScience · 2026Article
- SMAD7-Associated Glycolytic Regulation Promotes Lactate-Dependent Macrophage Phenotype Modulation in Colorectal Cancer.Cancers · 2026Article
- FSTL1 promotes M2 polarization of macrophages via the DIP2A-Smad2/3 Axis in gastric cancer.Journal of translational medicine · 2026Article
- CD47 and FOXP3Cancers · 2026Review
- Unraveling RELA as a potential dioctyl terephthalate-related target regulates M2-like macrophages to induce an immunosuppressive microenvironment in colorectal cancer: a multi-omics data study by experimental validation.Molecular diversity · 2026Article
- Comprehensive bioinformatics analysis of NCAPH expression and its clinical importance in endometrial cancer.Oncology letters · 2026Article
- Tumor cell-intrinsic TET3 restrains type I interferon signaling and anti-tumor immunity.Science China. Life sciences · 2026Article
- TTK Overexpression as a Prognostic Indicator and Immune Modulator in Kidney Renal Clear Cell Carcinoma.Molecular carcinogenesis · 2026Article
- Tumor-derived stearic acid induces macrophage Egr2 signaling to suppress anti-tumor immunity in breast cancer.bioRxiv : the preprint server for biology · 2026Article
- MRPL13 sustains mitochondrial integrity and MAPK-associated aggressiveness in esophageal squamous cell carcinoma.Cancer cell international · 2026Article
- NKG2A-HLA-E and TIM3-galectin 9 pathways promote immune inhibition and represent therapeutic vulnerabilities in pancreatic ductal adenocarcinoma.Cancer immunology, immunotherapy : CII · 2026Article
- Pan-cancer multi-omics analysis identifies TOMM22 as an oncogenic driver and therapeutic target in LIHC via ferroptosis regulation.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Comparative Interactome Analysis Reveals Architectural Principles Governing KInternational journal of molecular sciences · 2026Article
- Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.