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Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer

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  • Balázs Győrffy
  • Pawel Surowiak
  • Jan Budczies
  • András Lánczky

Abstract

In the last decade, optimized treatment for non-small cell lung cancer had lead to improved prognosis, but the overall survival is still very short. To further understand the molecular basis of the disease we have to identify biomarkers related to survival. Here we present the development of an online tool suitable for the real-time meta-analysis of published lung cancer microarray datasets to identify biomarkers related to survival. We searched the caBIG, GEO and TCGA repositories to identify samples with published gene expression data and survival information. Univariate and multivariate Cox regression analysis, Kaplan-Meier survival plot with hazard ratio and logrank P value are calculated and plotted in R. The complete analysis tool can be accessed online at: www.kmplot.com/lung. All together 1,715 samples of ten independent datasets were integrated into the system. As a demonstration, we used the tool to validate 21 previously published survival associated biomarkers. Of these, survival was best predicted by CDK1 (p

Suggested Citation

  • Balázs Győrffy & Pawel Surowiak & Jan Budczies & András Lánczky, 2013. "Online Survival Analysis Software to Assess the Prognostic Value of Biomarkers Using Transcriptomic Data in Non-Small-Cell Lung Cancer," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-8, December.
    • Handle: RePEc:plo:pone00:0082241
    DOI: 10.1371/journal.pone.0082241
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    1. Ming Yi & Ruoqing Zhu & Robert M Stephens, 2018. "GradientScanSurv—An exhaustive association test method for gene expression data with censored survival outcome," PLOS ONE, Public Library of Science, vol. 13(12), pages 1-28, December.
    2. Zhen Lu & Jinyun Chen & Pengfei Yu & Matthew J. Atherton & Jun Gui & Vivek S. Tomar & Justin D. Middleton & Neil T. Sullivan & Sunil Singhal & Subin S. George & Ashley G. Woolfork & Aalim M. Weljie & , 2022. "Tumor factors stimulate lysosomal degradation of tumor antigens and undermine their cross-presentation in lung cancer," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    3. Paul A Stewart & Katja Parapatics & Eric A Welsh & André C Müller & Haoyun Cao & Bin Fang & John M Koomen & Steven A Eschrich & Keiryn L Bennett & Eric B Haura, 2015. "A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-18, November.
    4. Bo Yuan & Jingyuan Xiong & Chaoxiong Zhang & Yuqin Yao & Chaoxiong Zhang & Ting An & Jie Liu, 2020. "Prognostic Roles of APLNR Expression in Non-Small Cell Lung Cancer," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 27(5), pages 21089-21098, May.
    5. Yongyao Fu & Abigail Pajulas & Jocelyn Wang & Baohua Zhou & Anthony Cannon & Cherry Cheuk Lam Cheung & Jilu Zhang & Huaxin Zhou & Amanda Jo Fisher & David T. Omstead & Sabrina Khan & Lei Han & Jean-Ch, 2022. "Mouse pulmonary interstitial macrophages mediate the pro-tumorigenic effects of IL-9," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    6. Lijuan Zhang & Kai Zhang & Jieyou Zhang & Jinrong Zhu & Qing Xi & Huafeng Wang & Zimu Zhang & Yingnan Cheng & Guangze Yang & Hongkun Liu & Xiangdong Guo & Dongmei Zhou & Zhenyi Xue & Yan Li & Qi Zhang, 2021. "Loss of fragile site-associated tumor suppressor promotes antitumor immunity via macrophage polarization," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    7. Jiang-jiang Li & Tiantian Yu & Peiting Zeng & Jingyu Tian & Panpan Liu & Shuang Qiao & Shijun Wen & Yumin Hu & Qiao Liu & Wenhua Lu & Hui Zhang & Peng Huang, 2024. "Wild-type IDH2 is a therapeutic target for triple-negative breast cancer," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    8. Eui Jung Moon & Stephano S. Mello & Caiyun G. Li & Jen-Tsan Chi & Kaushik Thakkar & Jacob G. Kirkland & Edward L. Lagory & Ik Jae Lee & Anh N. Diep & Yu Miao & Marjan Rafat & Marta Vilalta & Laura Cas, 2021. "The HIF target MAFF promotes tumor invasion and metastasis through IL11 and STAT3 signaling," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    9. Elena Spina & Julia Simundza & Angela Incassati & Anupama Chandramouli & Matthias C. Kugler & Ziyan Lin & Alireza Khodadadi-Jamayran & Christine J. Watson & Pamela Cowin, 2022. "Gpr125 is a unifying hallmark of multiple mammary progenitors coupled to tumor latency," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

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