SASD: the Synthetic Alternative Splicing Database for identifying novel isoform from proteomics

Area of Science:

• Proteomics
• Molecular Biology
• Bioinformatics

Background:

• Alternative splicing generates protein diversity and regulates expression.
• Protein-level analysis of alternative splicing offers advantages over mRNA-level analysis.
• Combining alternative splicing databases with mass spectrometry is key for novel isoform discovery.

Purpose of the Study:

• To create a comprehensive synthetic alternative splicing database (SASD).
• To identify and analyze novel alternative splicing protein isoforms.
• To interpret identified isoforms within pathways, diseases, drugs, and organs.

Main Methods:

• A three-step pipeline was employed to construct the SASD.
• Gene structure information from Ensembl Genes 71 and pathway data were integrated.
• Artificial splicing transcripts were compiled and translated into peptides.

Main Results:

• The SASD was successfully created to identify novel alternative splicing isoforms.
• The database enables interpretation of isoforms in specific biological contexts.
• The pipeline focused exclusively on alternative splicing for maximum coverage.

Conclusions:

• The SASD offers an efficient method for identifying and analyzing novel protein isoforms.
• It facilitates the characterization of Exon Skipping and Intron Retention events.
• The database supports interpretation within disease, drug, and organ-specific contexts.