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引用次数: 0
摘要
在这项研究中,我们介绍了通过整合基于单参考的解旋来稳健估计细胞类型比例的创新框架--ReCIDE(Robust estimation of Cell type proportions by Integrating single-reference-based DEconvolutions)。ReCIDE 在基准数据集和真实数据集中的表现优于现有方法,尤其是在估计罕见细胞类型比例方面。通过使用 ReCIDE 对三阴性乳腺癌(TNBC)患者的公开批量数据进行探索性分析,我们证明 TNBC 患者的预后与 T 细胞和血管周围样细胞亚型的比例之间存在显著的相关性。基于这一发现,我们建立了 TNBC 患者预后评估模型。我们的贡献是提出了一个提高解卷积准确性的新框架,展示了其在医学研究中的有效性。
ReCIDE: robust estimation of cell type proportions by integrating single-reference-based deconvolutions.
In this study, we introduce Robust estimation of Cell type proportions by Integrating single-reference-based DEconvolutions (ReCIDE), an innovative framework for robust estimation of cell type proportions by integrating single-reference-based deconvolutions. ReCIDE outperforms existing approaches in benchmark and real datasets, particularly excelling in estimating rare cell type proportions. Through exploratory analysis on public bulk data of triple-negative breast cancer (TNBC) patients using ReCIDE, we demonstrate a significant correlation between the prognosis of TNBC patients and the proportions of both T cell and perivascular-like cell subtypes. Built upon this discovery, we develop a prognostic assessment model for TNBC patients. Our contribution presents a novel framework for enhancing deconvolution accuracy, showcasing its effectiveness in medical research.
期刊介绍:
Briefings in Bioinformatics is an international journal serving as a platform for researchers and educators in the life sciences. It also appeals to mathematicians, statisticians, and computer scientists applying their expertise to biological challenges. The journal focuses on reviews tailored for users of databases and analytical tools in contemporary genetics, molecular and systems biology. It stands out by offering practical assistance and guidance to non-specialists in computerized methodologies. Covering a wide range from introductory concepts to specific protocols and analyses, the papers address bacterial, plant, fungal, animal, and human data.
The journal's detailed subject areas include genetic studies of phenotypes and genotypes, mapping, DNA sequencing, expression profiling, gene expression studies, microarrays, alignment methods, protein profiles and HMMs, lipids, metabolic and signaling pathways, structure determination and function prediction, phylogenetic studies, and education and training.