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基于基因表达数据的肺癌预后聚类方法的比较研究。

A comparative study of clustering methods on gene expression data for lung cancer prognosis.

机构信息

Wake Forest University, Winston-Salem, NC, United States of America.

Markey Cancer Center, University of Kentucky, Lexington, KY, USA.

出版信息

BMC Res Notes. 2023 Nov 8;16(1):319. doi: 10.1186/s13104-023-06604-8.

Abstract

Lung cancer subtyping based on gene expression data is important for identifying patient subgroups with differing survival prognosis to facilitate customized treatment strategies for each subtype of patients. Unsupervised clustering methods are the traditional approach for clustering patients into subtypes. However, since those methods cluster patients based only on gene expression data, the resulting clusters may not always be relevant to the survival outcome of interest. In recent years, semi-supervised and supervised methods have been proposed, which leverage the survival outcome data to identify clusters more relevant to survival prognosis. This paper aims to compare the performance of different clustering methods for identifying clinically prognostic lung cancer subtypes based on two lung adenocarcinoma datasets. For each method, we clustered patients into two clusters and assessed the difference in patient survival time between clusters. Unsupervised methods were found to have large logrank p-values and no significant results in most cases. Semi-supervised and supervised methods had improved performance over unsupervised methods and very significant p-values. These results indicate that unsupervised methods are not capable of identifying clusters with significant differences in survival prognosis in most cases, while supervised and semi-supervised methods can better cluster patients into clinically useful subtypes.

摘要

基于基因表达数据的肺癌亚型分类对于识别具有不同生存预后的患者亚组很重要,有助于为每个患者亚型制定定制化的治疗策略。无监督聚类方法是聚类患者为亚型的传统方法。然而,由于这些方法仅基于基因表达数据对患者进行聚类,因此得到的聚类结果可能并不总是与感兴趣的生存结果相关。近年来,提出了半监督和监督方法,利用生存结果数据来识别与生存预后更相关的聚类。本文旨在比较基于两个肺腺癌数据集的不同聚类方法在识别具有临床预后意义的肺癌亚型方面的性能。对于每种方法,我们将患者聚类为两个聚类,并评估聚类之间患者生存时间的差异。无监督方法的对数秩 p 值较大,在大多数情况下没有显著结果。半监督和监督方法的性能优于无监督方法,p 值非常显著。这些结果表明,在大多数情况下,无监督方法无法识别生存预后存在显著差异的聚类,而监督和半监督方法可以更好地将患者聚类为具有临床意义的亚型。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/624f/10630994/9204065ef254/13104_2023_6604_Fig1_HTML.jpg

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