Database for Identifying Exon Skipping Events
Author Information
Author(s): Mo Fan, Hong Xu, Gao Feng, Du Lin, Wang Jun, Omenn Gilbert S, Lin Biaoyang
Primary Institution: Zhejiang University
Hypothesis
Can a new exon-exon junction database improve the identification of novel alternative splicing events using mass spectrometry data?
Conclusion
The exon-exon junction database allows for efficient identification of novel alternatively spliced protein isoforms from mass spectrometry data.
Supporting Evidence
- The database contains 873,024 entries representing all compatible exon-exon junction sequences.
- Using liver cancer MS/MS data, 488 non-redundant peptides representing putative exon skipping events were identified.
- The approach identified a substantial number of novel alternative splicing junction sequences not defined in public databases.
Takeaway
Scientists created a special database to help find new ways genes can be mixed up to make different proteins, using data from mass spectrometry.
Methodology
Scripts were written in Perl, Bioperl, MySQL, and Ensembl API to build a theoretical exon-exon junction protein database and identify peptides from mass spectrometry data.
Limitations
The database is limited to known exons and cannot identify splicing involving unannotated exons or genes.
Digital Object Identifier (DOI)
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