ArticleCommunications biology2023
PUREE: accurate pan-cancer tumor purity estimation from gene expression data.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- Very low-carbohydrate ketogenic diet in treatment-naïve women with endometrial cancer and overweight: a randomized feasibility study.Nature communications · 2026Trial
- CDState Resolves Malignant Cell Heterogeneity from Bulk Tumor RNA Sequencing Data.Cancer research · 2026Article
- Antibody-drug conjugate engineering: from design to efficacy and safety.Signal transduction and targeted therapy · 2026Review
- Article
- Identification of key genes as diagnostic biomarkers for lung adenocarcinoma using bioinformatics and machine learning.Discover oncology · 2026Article
- CSsingle: a unified tool for robust decomposition of bulk and spatial transcriptomic data across diverse single-cell references.Nucleic acids research · 2026Article
- Therapeutic efficacy of dendritic cell vaccination in a novel syngeneic mouse model of diffuse hemispheric glioma, H3 G34-mutant.Journal of neuro-oncology · 2026Article
- A Pan-Cancer Single-Cell Atlas to Evaluate Tumor Identity, Cell Line Concordance, and Dependency Mapping.bioRxiv : the preprint server for biology · 2026Article
- Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.Neuro-oncology · 2026Article
- Integrative genomic and immune landscape analysis of intimal sarcomas for emerging therapeutic targets and immunotherapy strategies.Frontiers in immunology · 2026Article
- High BRAF variant allele frequency predicts poor outcomes in metastatic melanoma patients treated with BRAF/MEK inhibitors.Journal of translational medicine · 2025Article
- Reproducible autosomal gene expression changes with loss of typical X and Y complement across tumor types.bioRxiv : the preprint server for biology · 2025Article
- Human Papillomavirus Integration Induces Oncogenic Host Gene Fusions in Oropharyngeal Cancers.Cancer discovery · 2025Article
- GBMPurity: A machine learning tool for estimating glioblastoma tumor purity from bulk RNA-sequencing data.Neuro-oncology · 2025Article
- Single-Cell Transcriptomic Analysis Unveils Key Regulators and Signaling Pathways in Lung Adenocarcinoma Progression.Biomedicines · 2025Article
- Integrated transcriptomic landscape of medulloblastoma and ependymoma reveals novel tumor subtype-specific biology.bioRxiv : the preprint server for biology · 2025Article
- The 3D genome of plasma cells in multiple myeloma.Scientific reports · 2025Article
- A coregulatory influence map of glioblastoma heterogeneity and plasticity.NPJ precision oncology · 2025Article
- Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2-positive early breast cancer (EBC).Annals of oncology : official journal of the European Society for Medical Oncology · 2025Article
- Identification of Fanconi anemia pathway genes as novel prognostic biomarkers and therapeutic targets for breast cancer.Translational cancer research · 2025Article
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Authors and funding
4 authors.
Funding
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Abstract
Tumors are complex masses composed of malignant and non-malignant cells. Variation in tumor purity (proportion of cancer cells in a sample) can both confound integrative analysis and enable studies of tumor heterogeneity. Here we developed PUREE, which uses a weakly supervised learning approach to infer tumor purity from a tumor gene expression profile. PUREE was trained on gene expression data and genomic consensus purity estimates from 7864 solid tumor samples. PUREE predicted purity with high accuracy across distinct solid tumor types and generalized to tumor samples from unseen tumor types and cohorts. Gene features of PUREE were further validated using single-cell RNA-seq data from distinct tumor types. In a comprehensive benchmark, PUREE outperformed existing transcriptome-based purity estimation approaches. Overall, PUREE is a highly accurate and versatile method for estimating tumor purity and interrogating tumor heterogeneity from bulk tumor gene expression data, which can complement genomics-based approaches or be used in settings where genomic data is unavailable.
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