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Journal of Zhejiang University SCIENCE B

ISSN 1673-1581(Print), 1862-1783(Online), Monthly

2022 Vol.23 No.3 P.249-257

OShnscc: a novel user-friendly online survival analysis tool for head and neck squamous cell carcinoma based on RNA expression profiles and long-term survival information

Guosen ZHANG, Qiang WANG, Xinlei QI, Huimin YANG, Xiaodong SU, Manman YANG, Chao JIANG, Yang AN, Hong ZHENG, Lu ZHANG, Wan ZHU, Jiancheng GUO, Xiangqian GUO

Department of Predictive Medicine, Institute of Biomedical Informatics, Cell Signal Transduction Laboratory, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China; School of Software, Henan University, Kaifeng 475004, China; Department of Anesthesia, Stanford University, Stanford, CA 94305, USA; Department of Molecular Pathology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China; Precision Medicine Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China; Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450052, China

xqguo@henu.edu.cn, gjc@zzu.edu.cn

Abstract: Head and neck squamous cell carcinoma (HNSCC), as the most common type (>90%) of head and neck cancer, includes various epithelial malignancies that arise in the nasal cavity, oral cavity, pharynx, and larynx. In 2020, approximately 878 ‍ 000 new cases and 444 000 deaths linked to HNSCC occurred worldwide (Sung et al., 2021). Due to the associated frequent recurrence and metastasis, HNSCC patients have poor prognosis with a five-year survival rate of 40%–50% (Jou and Hess, 2017). Therefore, novel prognostic biomarkers need to be developed to identify high-risk HNSCC patients and improve their disease outcomes.

Key words: Head and neck squamous cell carcinoma; Prognostic biomarker; Online survival tool; Kaplan-Meier curve; OShnscc

Chinese Summary  <29> OShnscc：一个基于表达谱数据及其长期生存信息开发的头颈鳞癌在线生存分析工具

目的：头颈鳞癌是常见的恶性肿瘤之一，预后较差。开发新的预后分子标志物对于改善头颈鳞癌患者的预后具有重要意义。因此，本研究通过整合公共癌症数据库中的头颈鳞癌表达谱数据及临床生存信息，开发了头颈鳞癌在线生存分析工具OShnscc（Online consensus Survival tool for Head and Neck Squamous Cell Carcinoma），用于评价基因mRNA表达量与头颈鳞癌患者生存时间的相关性。
创新点：本研究开发的OShnscc是目前为止包含头颈鳞癌预后数据集最多、样本量最大的在线生存分析工具。用户不仅可以在多个独立数据集中分析和比较基因的预后价值，还可以利用多种临床因素如肿瘤TNM分期、肿瘤分级、年龄、性别等因素作为筛选条件进行亚组预后分析。
方法：OShnscc的开发包括三部分：（1）以样本为人头颈鳞癌临床样本的基因芯片或二代测序数据且数据集样本数大于20个为筛选标准，从公共癌症数据库中收集和筛选有效的头颈鳞癌数据集；（2）使用SQL Server 2008对样本头颈鳞癌表达谱数据与样本生存时间进行回归分析，构建头颈鳞癌预后数据库；（3）采用Java语言开发在线分析系统，使用R语言进行生存分析，应用R sever服务进行Java语言与R语言的连接。
结论：OShnscc是一个公开免费的在线生存分析工具（网址：http://bioinfo.henu.edu.cn/HNSC/HNSCList.jsp），为缺少生物信息学背景的医学及相关科研人员提供一个快速分析基因mRNA表达量与头颈鳞癌患者预后关系的平台，有助于推动头颈鳞癌的预后标志物开发。

关键词组：头颈鳞癌；在线生存分析工具；预后标志物


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DOI:

10.1631/jzus.B2100512

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2024-08-27

Received:

2023-10-17

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2024-05-08

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