%0 Journal Article
%T In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity
%A Francisco J Ossandon
%A Cynthia Villarroel
%A Francisco Aguayo
%A Eudocia Santibanez
%A Naohide Oue
%A Wataru Yasui
%A Alejandro H Corvalan
%J Molecular Cancer
%D 2008
%I BioMed Central
%R 10.1186/1476-4598-7-22
%X Gastric carcinoma is the second leading cause of cancer-related death worldwide and has marked geographical variations [1-3]. The observed advantage in 5-year survival rate from patients from the East than from the West may reflect differences in diagnostic criteria, better staging methods and more radical surgery [4]. However emerging evidence supports the concept that ethnicity might contribute to the disparate gastric carcinoma outcomes between the East and the West [4,5]. Serial Analysis of Gene Expression (SAGE) is a comprehensive profiling method that allows for global, unbiased and quantitative characterization of transcriptomes [6]. A major advantage of SAGE is that once normalized is possible to directly compare the levels of tags generated by a single experiment with any other available [7]. To gain an insight of the differences between gastric carcinoma transcriptomes that might explain the disparate outcomes between the East and the West here we compare datasets of fifteen SAGE libraries derived from normal and gastric tumor tissues from Japanese and American gastric cancer patients by Correspondence Analysis, Support Tree and Significance Analysis for Microarray for significative tags and gene selection. We found specific genes differentially expressed between normal and tumor SAGE libraries as well as tumor libraries from the East and the West. These differentially expressed genes could explain the worse survival rate in the West in comparison to the East.Fifteen gastric SAGE libraries (4 normal and 11 tumor) from Cancer Genome Anatomy Project (CGAP) [7] were combined for the analysis. Only libraries with 10 bp tags and the same cutting enzymes (BsmFI and NlaIII) were included in this study. Normal libraries consist of a tissue pool (GSM784 and GSM14780) or microdissected samples (CGAP_MD_13S and CGAP_MD_14S) and were produced by El-Rifai et al [8] in Virginia, USA. Gastric tumor libraries consist of five libraries, three microdissected (CGAP_MD_HG7, C
%U http://www.molecular-cancer.com/content/7/1/22