Transposable elements in human cancers by genome-wide EST alignment.

Abstract

Transposable elements may affect coding sequences, splicing patterns, and transcriptional regulation of human genes. Particles of the transposable elements have been detected in several tissues and tumors. Here, we report genome-wide analysis of gene expression regulated by transposable elements in human cancers. We adopted an analysis pipeline for screening methods to detect cancer-specific expression from expressed human sequences. We developed a database (TECESdb) for understanding the mechanism of cancer development in relation to transposable elements. A total of 999 genes fused with transposable elements were found to be cancer-related in our analysis of the EST database. According to GO (Gene Ontology) analysis, the majority of the 999 cancer-specific genes have functional association with gene receptor, DNA binding, and kinase activity. Our data could contribute greatly to our understanding of human cancers in relation to transposable elements.

• Authors: Dae-Soo Kim, Jae-Won Huh, Heui-Soo Kim
• Journal: Genes & genetic systems (Genes Genet Syst) Vol. 82 Issue 2 Pg. 145-56 (Apr 2007) ISSN: 1341-7568 [Print] Japan
• PMID: 17507780 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• DNA Transposable Elements
• DNA, Neoplasm
• RNA, Neoplasm
• Recombinant Fusion Proteins

Topics

• Algorithms
• DNA Transposable Elements (physiology)
• DNA, Neoplasm (analysis)
• Databases, Genetic
• Expressed Sequence Tags
• Gene Expression Regulation, Neoplastic
• Genome, Human
• Humans
• Neoplasms (etiology, genetics)
• RNA, Neoplasm (analysis)
• Recombinant Fusion Proteins (genetics)
• Sequence Alignment
• Software