TRANSCRIPTOME 2002: From Functional Genomics to Systems
Expression Profiling and TPE Analysis Generates Candidate Tumor Markers for Papillary Thyroid Carcinoma
Erwin Pauws1, Truus JM Veenboer1, Antoine HC van Kampen2, Jan JM de Vijlder1, Carrie Ris-Stalpers1, 1Pediatric Endocrinology, Amsterdam, THE NETHERS-LANDS, 2Bioinformatics Laboratory, Academic Medical Center, Amsterdam, THE NETHERLANDS
Using Serial Expression of Gene Expression (SAGE) the expression profiles of normal thyroid and papillary thyroid carcinoma are compared. Each profile consists of 10,000 tags corresponding to 6,000 unique transcripts. Substraction generates 22 upregulated transcripts and 121 downregulated transcripts (p<0.05). An algorithm is developed to calculate a Tissue Preferential Expression (TPE) value of these differentially expressed transcripts, comparing the expression of each tag to the expression of that tag in a cohort of SAGE libraries from normal and neoplastic tissues publicly available at NCBI/CGAP. A high TPE value (range 0-100) indicates specific expression in the primary library compared to the cohort. Ordering the differentially expressed transcripts according tot their TPE value shows that transcripts like XPC and ECM1 are specifically upregulated in thyroid carcinoma while transcripts like VEGF and CD9 are more generally expressed in tumor tissues. Confirmed downregulated thyroid specific transcripts like TG and TPO show high TPE values as expected. The role of the resulting shortlist of transcripts in the initiation and/or progression of thyroid cancer is now under investigation. SAGE analysis and subsequent determination of TPE value fascilitates the rapid distinction of genes specifically expressed in cancer tissues in general, or in a specific tumor tissue.
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