CBioProfiler:A Web and Standalone Pipeline for Cancer Biomarker and Subtype Characterization  

作　　者：Xiaoping Liu Zisong Wang Hongjie Shi Sheng Li Xinghuan Wang 

机构地区：[1]Department of Urology,Zhongnan Hospital of Wuhan University,Wuhan 430071,China [2]Department of Pathology,Zhongnan Hospital of Wuhan University,Wuhan 430071,China [3]Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center,Zhongnan Hospital of Wuhan University,Wuhan 430071,China [4]Department of Biological Repositories,Zhongnan Hospital of Wuhan University,Wuhan 430071,China

出　　处：《Genomics, Proteomics & Bioinformatics》2024年第3期153-165,共13页基因组蛋白质组与生物信息学报（英文版）

摘　　要：Cancer is a leading cause of death worldwide,and the identification of biomarkers and subtypes that can predict the long-term survival of cancer patients is essential for their risk stratification,treatment,and prognosis.However,there are currently no standardized tools for exploring cancer biomarkers or subtypes.In this study,we introduced Cancer Biomarker and subtype Profiler(CBioProfiler),a web server and standalone application that includes two pipelines for analyzing cancer biomarkers and subtypes.The cancer biomarker pipeline consists of five modules for identifying and annotating cancer survival-related biomarkers using multiple survival-related machine learning algorithms.The cancer subtype pipeline includes three modules for data preprocessing,subtype identification using multiple unsupervised machine learning methods,and subtype evaluation and validation.CBioProfiler also includes CuratedCancerPrognosisData,a novel R package that integrates reviewed and curated gene expression and clinical data from 268 studies.These studies cover 43 common blood and solid tumors and draw upon 47,686 clinical samples.The web server is available at https://www.cbioprofiler.com/and https://cbioprofiler.znhospital.cn/CBioProfiler/,and the standalone app and source code can be found at https://github.com/liuxiaoping2020/CBioProfiler.

关 键 词：CBioProfiler Cancer biomarker Cancer subtype Machine learning Web app 

分 类 号：Q811.4[生物学—生物工程]