Zeng H, Zheng R, Zhang S, Zuo T, Xia C, Zou X, Chen W. Esophageal cancer statistics in China, 2011: estimates based on 177 cancer registries. Thorac Cancer. 2016;7:232–7.
Article
PubMed
Google Scholar
Chen W, Zheng R, Baade PD, Zhang S, Zeng H, Bray F, Jemal A, Yu XQ, He J. Cancer statistics in China, 2015. CA Cancer J Clin. 2016;66(2):115–32.
Article
PubMed
Google Scholar
Takeno S, Noguchi T, Takahashi Y, Fumoto S, Shibata T, Kawahara K. Assessment of clinical outcome in patients with esophageal squamous cell carcinoma using TNM classification score and molecular biological classification. Ann Surg Oncol. 2007;14:1431–8.
Article
PubMed
Google Scholar
Wohlschlager J, Wittekind C, Theegarten D. New TNM classification of malignant lung tumours. Pathologe. 2010;31:355–60.
Article
PubMed
CAS
Google Scholar
Magee JA, Piskounova E, Morrison SJ. Cancer stem cells: impact, heterogeneity, and uncertainty. Cancer Cell. 2012;21:283–96.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sobin LH, Fleming ID. TNM classification of malignant tumors. Cancer. 1997;80:1803–4.
Article
PubMed
CAS
Google Scholar
Sobin LH, Hermanek P, Hutter RV. TNM classification of malignant tumors. A comparison between the new (1987) and the old editions. Cancer. 1988;61:2310–4.
Article
PubMed
CAS
Google Scholar
Kunisaki C, Akiyama H, Nomura M, Matsuda G, Otsuka Y, Ono HA, Shimada H. Developing an appropriate staging system for esophageal carcinoma. J Am Coll Surg. 2005;201:884–90.
Article
PubMed
Google Scholar
Goldstraw P, Chansky K, Crowley J, Rami-Porta R, Asamura H, Eberhardt WE, Nicholson AG, Groome P, Mitchell A, Bolejack V, et al. The IASLC lung cancer staging project: proposals for revision of the TNM stage groupings in the forthcoming (eighth) edition of the TNM classification for lung cancer. J Thorac Oncol. 2016;11:39–51.
Article
PubMed
Google Scholar
Varotti G, Ramacciato G, Ercolani G, Grazi GL, Vetrone G, Cescon M, Del Gaudio M, Ravaioli M, Ziparo V, Lauro A, et al. Comparison between the fifth and sixth editions of the AJCC/UICC TNM staging systems for hepatocellular carcinoma: multicentric study on 393 cirrhotic resected patients. Eur J Surg Oncol. 2005;31:760–7.
Article
PubMed
CAS
Google Scholar
Tripathy D, Harnden K, Blackwell K, Robson M. Next generation sequencing and tumor mutation profiling: are we ready for routine use in the oncology clinic? BMC Med. 2014;12:140.
Article
PubMed
PubMed Central
CAS
Google Scholar
Biesecker LG, Burke W, Kohane I, Plon SE, Zimmern R. Next-generation sequencing in the clinic: are we ready? Nat Rev Genet. 2012;13:818–24.
Article
PubMed
PubMed Central
CAS
Google Scholar
Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999;286:531–7.
Article
PubMed
CAS
Google Scholar
Wang SL, Sun L, Fang J. Molecular cancer classification using a meta-sample-based regularized robust coding method. BMC Bioinform. 2014;15(Suppl 15):S2.
Article
Google Scholar
Wang SL, Zhu YH, Jia W, Huang DS. Robust classification method of tumor subtype by using correlation filters. IEEE/ACM Trans Comput Biol Bioinform. 2012;9:580–91.
Article
PubMed
Google Scholar
Tan H, Zhang H, Xie J, Chen B, Wen C, Guo X, Zhao Q, Wu Z, Shen J, Wu J, et al. A novel staging model to classify oesophageal squamous cell carcinoma patients in China. Br J Cancer. 2014;110:2109–15.
Article
PubMed
PubMed Central
CAS
Google Scholar
Peters CJ, Rees JR, Hardwick RH, Hardwick JS, Vowler SL, Ong CA, Zhang C, Save V, O’Donovan M, Rassl D, et al. A 4-gene signature predicts survival of patients with resected adenocarcinoma of the esophagus, junction, and gastric cardia. Gastroenterology. 2010;139:1995–2004 (e15).
Article
PubMed
CAS
Google Scholar
Nielsen TO, Parker JS, Leung S, Voduc D, Ebbert M, Vickery T, Davies SR, Snider J, Stijleman IJ, Reed J, et al. A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res. 2010;16:5222–32.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wang W, Wang Z, Zhao J, Wei M, Zhu X, He Q, Ling T, Chen X, Cao Z, Zhang Y, et al. A novel molecular and clinical staging model to predict survival for patients with esophageal squamous cell carcinoma. Oncotarget. 2016;7(39):63526.
PubMed
PubMed Central
Google Scholar
Sawada T, Yashiro M, Sentani K, Oue N, Yasui W, Miyazaki K, Kai K, Fushida S, Fujimura T, Ohira M, et al. New molecular staging with G-factor supplements TNM classification in gastric cancer: a multicenter collaborative research by the Japan Society for Gastroenterological Carcinogenesis G-Project committee. Gastric Cancer. 2015;18:119–28.
Article
PubMed
CAS
Google Scholar
Sveen A, Agesen TH, Nesbakken A, Meling GI, Rognum TO, Liestol K, Skotheim RI, Lothe RA. ColoGuidePro: a prognostic 7-gene expression signature for stage III colorectal cancer patients. Clin Cancer Res. 2012;18:6001–10.
Article
PubMed
CAS
Google Scholar
Zhang HF, Chen Y, Wu C, Wu ZY, Tweardy DJ, Alshareef A, Liao LD, Xue YJ, Wu JY, Chen B, et al. The opposing function of STAT3 as an oncoprotein and tumor suppressor is dictated by the expression status of STAT3beta in esophageal squamous cell carcinoma. Clin Cancer Res. 2016;22:691–703.
Article
PubMed
CAS
Google Scholar
Xie JJ, Guo JC, Wu ZY, Xu XE, Wu JY, Chen B, Ran LQ, Liao LD, Li EM, Xu LY. Integrin α5 promotes tumor progression and is an independent unfavorable prognostic factor in esophageal squamous cell carcinoma. Hum Pathol. 2016;48:69–75.
Article
PubMed
CAS
Google Scholar
Shang L, Hao JJ, Zhao XK, He JZ, Shi ZZ, Liu HJ, Wu LF, Jiang YY, Shi F, Yang H, et al. ANO1 protein as a potential biomarker for esophageal cancer prognosis and precancerous lesion development prediction. Oncotarget. 2016;7:24374–82.
PubMed
PubMed Central
Google Scholar
Sun LL, Wu JY, Wu ZY, Shen JH, Xu XE, Chen B, Wang SH, Li EM, Xu LY. A three-gene signature and clinical outcome in esophageal squamous cell carcinoma. Int J Cancer. 2015;136:E569–77.
Article
PubMed
CAS
Google Scholar
Cao HH, Zhang SY, Shen JH, Wu ZY, Wu JY, Wang SH, Li EM, Xu LY. A three-protein signature and clinical outcome in esophageal squamous cell carcinoma. Oncotarget. 2015;6:5435–48.
PubMed
Google Scholar
Xie JJ, Xie YM, Chen B, Pan F, Guo JC, Zhao Q, Shen JH, Wu ZY, Wu JY, Xu LY, et al. ATF3 functions as a novel tumor suppressor with prognostic significance in esophageal squamous cell carcinoma. Oncotarget. 2014;5:8569–82.
PubMed
PubMed Central
Google Scholar
Hou J, Liao LD, Xie YM, Zeng FM, Ji X, Chen B, Li LY, Zhu MX, Yang CX, Qing Z, et al. DACT2 is a candidate tumor suppressor and prognostic marker in esophageal squamous cell carcinoma. Cancer Prev Res. 2013;6:791–800.
Article
CAS
Google Scholar
Lin RJ, Xiao DW, Liao LD, Chen T, Xie ZF, Huang WZ, Wang WS, Jiang TF, Wu BL, Li EM, et al. MiR-142-3p as a potential prognostic biomarker for esophageal squamous cell carcinoma. J Surg Oncol. 2012;105:175–82.
Article
PubMed
CAS
Google Scholar
Gibb EA, Brown CJ, Lam WL. The functional role of long non-coding RNA in human carcinomas. Mol Cancer. 2011;10:38.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010;464:1071–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kong H, Wu Y, Zhu M, Zhai C, Qian J, Gao X, Wang S, Hou Y, Lu S, Zhu H. Long non-coding RNAs: novel prognostic biomarkers for liver metastases in patients with early stage colorectal cancer. Oncotarget. 2016;7(31):50428.
PubMed
PubMed Central
Google Scholar
Fan Q, Liu B. Identification of a RNA-Seq based 8-long non-coding RNA signature predicting survival in esophageal cancer. Med Sci Monit. 2016;22:5163–72.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gao SY, Li EM, Cui L, Lu XF, Meng LY, Yuan HM, Xie JJ, Du ZP, Pang JX, Xu LY. Sp1 and AP-1 regulate expression of the human gene VIL2 in esophageal carcinoma cells. J Biol Chem. 2009;284:7995–8004.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhang XD, Xie JJ, Liao LD, Long L, Xie YM, Li EM, Xu LY. 12-O-tetradecanoylphorbol-13-acetate induces up-regulated transcription of variant 1 but not variant 2 of VIL2 in esophageal squamous cell carcinoma cells via ERK1/2/AP-1/Sp1 signaling. PLoS ONE. 2015;10:e0124680.
Article
PubMed
PubMed Central
CAS
Google Scholar
Llorens-Bobadilla E, Zhao S, Baser A, Saiz-Castro G, Zwadlo K, Martin-Villalba A. Single-cell transcriptomics reveals a population of dormant neural stem cells that become activated upon brain injury. Cell Stem Cell. 2015;17:329–40.
Article
PubMed
CAS
Google Scholar
Wang A, Gehan EA. Gene selection for microarray data analysis using principal component analysis. Stat Med. 2005;24:2069–87.
Article
PubMed
Google Scholar
Crescenzi M, Giuliani A. The main biological determinants of tumor line taxonomy elucidated by a principal component analysis of microarray data. FEBS Lett. 2001;507:114.
Article
PubMed
CAS
Google Scholar
Charrad M, Ghazzali N, Boiteau V, Niknafs A. NbClust: an R package for determining the relevant number of clusters in a data set. BMC Health Serv Res. 2014;61:1–36.
Google Scholar
Team RDC. R: a language and environment for statistical computing. Computing. 2013;14:12–21.
Google Scholar
Landgrebe TCW, Duin RPW. Approximating the multiclass ROC by pairwise analysis. Pattern Recogn Lett. 2007;28:1747–58.
Article
Google Scholar
Landgrebe TCW, Duin RPW. Efficient multiclass ROC approximation by decomposition via confusion matrix perturbation analysis. IEEE Trans Pattern Anal Mach Intell. 2008;30:810–22.
Article
PubMed
Google Scholar
Therneau TM, Atkinson EJ. An introduction to recursive partitioning using the RPART routine technical report 61. Rochester: Mayo Foundation; 1997.
Google Scholar
Ripley B. Tree: classification and regression trees. Wiley Interdiscip Rev Data Mining Knowl Discov. 2011;1:14–23.
Article
Google Scholar
Becker RA, Chambers JM, Wilks AR. The new S language. Biometrics. 1988;45:935.
Google Scholar
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z, Galon J. ClueGO: a Cytoscape plug-into decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25:1091–3.
Article
PubMed
PubMed Central
CAS
Google Scholar
Guo JC, Li CQ, Wang QY, Zhao JM, Ding JY, Li EM, Xu LY. Protein-coding genes combined with long non-coding RNAs predict prognosis in esophageal squamous cell carcinoma patients as a novel clinical multi-dimensional signature. Mol BioSyst. 2016;12:3467–77.
Article
PubMed
CAS
Google Scholar
Li J, Chen Z, Tian L, Zhou C, He MY, Gao Y, Wang S, Zhou F, Shi S, Feng X, et al. LncRNA profile study reveals a three-lncRNA signature associated with the survival of patients with oesophageal squamous cell carcinoma. Gut. 2014;63:1700–10.
Article
PubMed
PubMed Central
CAS
Google Scholar
Naderi A, Teschendorff AE, Beigel J, Cariati M, Ellis IO, Brenton JD, Caldas C. BEX2 is overexpressed in a subset of primary breast cancers and mediates nerve growth factor/nuclear factor-κB inhibition of apoptosis in breast cancer cell lines. Cancer Res. 2007;67:6725–36.
Article
PubMed
CAS
Google Scholar
Hu ZQ, Zhou SL, Zhou ZJ, Luo CB, Chen EB, Zhan H, Wang PC, Dai Z, Zhou J, Fan J, et al. Overexpression of semaphorin 3A promotes tumor progression and predicts poor prognosis in hepatocellular carcinoma after curative resection. Oncotarget. 2016;7(32):51733.
Article
PubMed
PubMed Central
Google Scholar
Tang C, Gao X, Liu H, Jiang T, Zhai X. Decreased expression of SEMA3A is associated with poor prognosis in gastric carcinoma. Int J Clin Exp Pathol. 2014;7:4782–94.
PubMed
PubMed Central
CAS
Google Scholar
Leung YF, Cavalieri D. Fundamentals of cDNA microarray data analysis. Trends Genet. 2003;19:649–59.
Article
PubMed
CAS
Google Scholar
Shalon D, Smith SJ, Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 1996;6:639–45.
Article
PubMed
CAS
Google Scholar