Analysis of gene expression, alternative splicing and chromosomal translocation and their implications in cancer by expressed sequence tags

Abstract

As one of the major high-throughput gene expression databases, dbEST contains enormous amount of expression data from numerous tissues. Currently, there are about five million EST sequences of human origin in dbEST, and half of which were derived from tumor tissues. The random sampling nature of EST sequencing and sequencing length for each clone render EST data tremendous advantage in finding alternative splicing events, chromosomal translocation, and differential gene expression as well as their implications in cancer. In this study we have explored the feasibilities in using ESTs to gain cancer-related information and discussed the methodologies and related issues. Example results were presented on the up-regulation of rac1b, correlation of expression levels between non-muscle β- and γ-actins, and translocation events for TEL and AML1, as well as alternative splicing of CD44 as discovered by EST data analysis. Our study indicates that, with proper analysis, EST data could provide valuable information for the better understanding of tumorigenesis and cancer biology.