Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The . gov means it’s official. Federal government websites often end in . gov or VSports app下载. mil. Before sharing sensitive information, make sure you’re on a federal government site. .

Https

The site is secure. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely V体育官网. .

. 2013 Dec 18;8(12):e82241.
doi: 10.1371/journal.pone.0082241. eCollection 2013.

Online survival analysis software to assess the prognostic value of biomarkers using transcriptomic data in non-small-cell lung cancer (V体育平台登录)

Balázs Győrffy  1 , Pawel Surowiak  2 , Jan Budczies  3 , András Lánczky  1
Affiliations

Online survival analysis software to assess the prognostic value of biomarkers using transcriptomic data in non-small-cell lung cancer

Balázs Győrffy et al. PLoS One. .

Erratum in

  • PLoS One. 2014;9(10):e111842

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<1E-16), CD24 (p<1E-16) and CADM1 (p = 7E-12) in adenocarcinomas and by CCNE1 (p = 2. 3E-09) and VEGF (p = 3 VSports手机版. 3E-10) in all NSCLC patients. Additional genes significantly correlated to survival include RAD51, CDKN2A, OPN, EZH2, ANXA3, ADAM28 and ERCC1. In summary, we established an integrated database and an online tool capable of uni- and multivariate analysis for in silico validation of new biomarker candidates in non-small cell lung cancer. .

PubMed Disclaimer

V体育平台登录 - Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

"V体育官网入口" Figures

Figure 1
Figure 1. Survival characteristics of the patients included in the database including histology of adenocarcinoma (adeno), squamous cell carcinoma (SCC) and large cell carcinoma (large), gender, stage (only with overall survival) and smoking history.
Figure 2
Figure 2. Validation of 29 previously published NSCLC biomarkers.
Meta-analysis of these genes and signatures in the respective sample cohort yielded CCNE1, CDC2 and CADM1 as the best performing individual genes (A–C) and the signature of Yamauchi et al. (D). A funnel plot depicting the hazard ratios (with confidence intervals) versus sample number for CDC2 and VEGF shows more reliable estimation with larger database sizes (E–F).
See this image and copyright information in PMC

References (V体育平台登录)

    1. Siegel R, Naishadham D, Jemal A (2012) Cancer statistics, 2012. CA Cancer J Clin 62: 10–29. - PubMed
    1. Ramalingam SS, Owonikoko TK, Khuri FR (2011) Lung cancer: New biological insights and recent therapeutic advances. CA Cancer J Clin 61: 91–112. - PubMed
    1. Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, et al. (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc Natl Acad Sci U S A 98: 13790–13795. - PMC - PubMed
    1. Beer DG, Kardia SL, Huang CC, Giordano TJ, Levin AM, et al. (2002) Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 8: 816–824. - PubMed
    1. Lu Y, Lemon W, Liu PY, Yi Y, Morrison C, et al. (2006) A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. PLoS Med 3: e467. - PMC (V体育官网) - PubMed

"VSports手机版" Publication types