摘要
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。
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Acknowledgments
This work was supported by the National Natural Science Foundation of China (No. U2004136), the Supporting Program for Central Plain Young Top Talents (No. ZYQR201912176), the Program for Innovative Talents of Science and Technology in Henan Province (No. 18HASTIT048), the Program for Science and Technology Development in Henan Province (Nos. 212102310150, 202102310063, and SBGJ2018041), the Kaifeng Science and Technology Project (No. 1908001), and the Supporting Grant of Henan University (Nos. 2018YLJC01, 2019YLXKJC01, and 2020YLZDYJ14), China.
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Fig. S1; Tables S1–S3; Materials and methods
Materials and methods
Detailed methods are provided in the electronic supplementary materials of this paper.
Author contributions
Guosen ZHANG performed data collection, developed the web tool, and wrote and edited the manuscript. Qiang WANG and Xinlei QI performed data collection and developed the web tool. Huimin YANG, Xiaodong SU, Manman YANG, Chao JIANG, and Yang AN contributed to data collection and analysis. Hong ZHENG, Lu ZHANG, and Wan ZHU performed data analysis and paper writing. Jiancheng GUO and Xiangqian GUO contributed to the study design, data analysis, writing and editing of the manuscript. All authors have read and approved the final manuscript, and therefore, have full access to all the data in the study and take responsibility for the integrity and security of the data.
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Guosen ZHANG, Qiang WANG, Xinlei QI, Huimin YANG, Xiaodong SU, Manman YANG, Chao JIANG, Yang AN, Hong ZHENG, Lu ZHANG, Wan ZHU, Jiancheng GUO, and Xiangqian GUO declare that they have no conflict of interest.
This article does not contain any studies with human or animal subjects performed by any of the authors.
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Zhang, G., Wang, Q., Qi, X. et al. 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. J. Zhejiang Univ. Sci. B 23, 249–257 (2022). https://doi.org/10.1631/jzus.B2100512
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DOI: https://doi.org/10.1631/jzus.B2100512