TRANSCRIPTOME 2002: From Functional Genomics to Systems
ORESTES and the International Database of Cancer Gene Expression
André L. Vettore1, Anamaria A. Camargo1, Sandro J. de Souza1, Gregory J. Riggins2, Robert L. Strausberg3, Andrew J. G. Simpson1, 1Ludwig Institute for Cancer Research, São Paulo, BRAZIL, 2Duke University, Duham, NC, 3National Cancer Institute, Bethesda, MD.
Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central, protein-coding portion of transcripts. Up to now, over 740,000 ORESTES sequences from human normal and tumor tissues have been deposited in the GenBank database. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed human genes in the tumors studied. We thus believe that the capacity of the ORESTES strategy for gene discovery exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that is a useful alternative to full-length cDNA cloning.Using ESTs (expressed sequence tags), SAGE (serial analysis of gene expression) and ORESTES sequences, an International Database of Cancer Gene Expression has been assembled comprising six million gene tags (ORESTES, CGAP-ESTs and CGAP-SAGE), which reflect the expression gene profiles of a wide variety of cancerous and normal tissues. A suite of informatics tools has designed to facilitate analysis of these datasets and is available through the NCI Cancer Genome Anatomy Project web site (http://cgap.nci.nih.gov/).
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