Mining colon cancer specific alternative splicing in EST database
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- PMID: 16779299
- PMCID: PMC1560692
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Mining colon cancer specific alternative splicing in EST database
AMIA Annu Symp Proc.
2005.
Abstract
Among 75218 splicing sites, 137 colon cancer specific alternative splicing isoforms were found by mining EST database. Alternative splicing database were first constructed by aligning EST to genomic sequence. Numbers of ESTs from normal or cancer colon tissue supporting splicing isoform at each splicing site were then queried and analyzed with Fisher exact test. There were 53 3' splicing, 42 5' splicing, 40 exon skipping and 2 mutual exclusive cancer specific splicing isoforms.
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References
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- Patten LC, Belaguli NS, Baek MJ, Fagan SP, Awad SS, Berger DH. Serum response factor is alternatively spliced in human colon cancer. J Surg Res. 2004 Sep;121(1):92–100. - PubMed
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- Hsu FR, Chen JF. Aligning ESTs to genome using multi-layer unique markers. Proc. Of the IEEE Computational Systems Bioinformatics Conference (CSB2003). San Francisco, USA. 2003 Aug. p. 564–566.
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