ArticleBMC bioinformatics2008
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
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- Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome.Cell reports · 2019Article
- Computational identification of micro-structural variations and their proteogenomic consequences in cancer.Bioinformatics (Oxford, England) · 2018Article
- PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq.BMC bioinformatics · 2016Article
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
- Onco-proteogenomics: cancer proteomics joins forces with genomics.Nature methods · 2014Article
- Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics.Journal of proteome research · 2014Review
- Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.Molecular & cellular proteomics : MCP · 2013Article
- The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.Genomics · 2011Article
- Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data.BMC plant biology · 2011Article
- OryzaPG-DB: rice proteome database based on shotgun proteogenomics.BMC plant biology · 2011Article
- RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma.PloS one · 2011Article
- The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment.BMC bioinformatics · 2010Article
- SAW: a method to identify splicing events from RNA-Seq data based on splicing fingerprints.PloS one · 2010Article
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Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundAlternative 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.
resultsWe wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon 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 non-redundant peptides that represent putative exon skipping events.
conclusionOur exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data.
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