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...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Fan Mo, Xu Hong, Feng Gao, Lin Du, Jun Wang, Gilbert S. Omenn, Biaoyang Lin
• Keywords: Alternative Splicing, Alternative Splicing Events, BMCBI 2008, Multi-exon Human Genes