Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues

Genes differentially expressed in normal versus tumor tissues were identified using a computer-based differential display strategy. Bcl-xL, an anti-apoptotic member of the Bcl-2 family, was selected for confirmation by western blot analysis.Our genome-wide expression analysis identified a set of genes whose differential expression may be attributed to the genetic alterations associated with tumor formation and malignant growth. We propose complete lists of genes that may serve as targets for projects seeking novel candidates for cancer diagnosis and therapy. Our validation result showed increased protein levels of Bcl-xL in two different liver cancer specimens compared to normal liver. Notably, our EST-based data mining procedure indicated that most of the changes in gene expression observed in cancer cells corresponded to gene inactivation patterns. Chromosomes and chromosomal regions most frequently associated with aberrant expression changes in cancer libraries were also determined.Through the description of several candidates (including genes encoding extracellular matrix and ribosomal components, cytoskeletal proteins, apoptotic regulators, and novel tissue-specific biomarkers), our study illustrates the utility of in silico transcriptomics to identify tumor cell signatures, tumor-related genes and chromosomal regions frequently associated with aberrant expression in cancer.Large-scale transcriptome analysis of genes that are differently expressed in tumor tissues compared to their normal counterparts is an important route to the identification of candidates that could play a role in human malignancies. A number of techniques, ranging from differential display and nucleic acid subtraction to serial analysis of gene expression, expression microarrays and gene chips, have been used to the discovery of such aberrantly expressed cancer-related genes [1]. The well-established differential screening technology, that allows for the simultaneous comparison of multiple