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BMCBI
2008

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

10 years 11 months ago
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
Background: Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. Results: We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exonexon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 nonredundant peptides that represent putative exon skipping events. Conclusion: Our exon-exon junction database prov...
Fan Mo, Xu Hong, Feng Gao, Lin Du, Jun Wang, Gilbe
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Fan Mo, Xu Hong, Feng Gao, Lin Du, Jun Wang, Gilbert S. Omenn, Biaoyang Lin
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