Transposable elements in human cancers by genome-wide EST alignment.
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.
Kim
Dae-Soo
DS
PBBRC, Interdisciplinary Research Program of Bioinformatics, Pusan National University, Busan, Republic of Korea.
Huh
Jae-Won
JW
Kim
Heui-Soo
HS
D000465:Algorithms; D004251:DNA Transposable Elements / Q000502:physiology*; D004273:DNA, Neoplasm / Q000032:analysis; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms / Q000209:etiology / Q000235:genetics*; D012334:RNA, Neoplasm / Q000032:analysis; D011993:Recombinant Fusion Proteins / Q000235:genetics; D016415:Sequence Alignment; D012984:Software
D004251:DNA Transposable Elements; D004273:DNA, Neoplasm; D012334:RNA, Neoplasm; D011993:Recombinant Fusion Proteins