EXPANSION

EXPANSION analyzes protein-coding alternative splice variants to assess their functional consequences by integrating differentially expressed transcript data with protein domain, post-translational modification, and protein–protein interaction information.

Key Features:

• Data Integration: Integrates differentially expressed (DE) protein-coding transcript data from cancer genomics with domain architecture, protein interaction networks, and gene enrichment analyses.
• Domain Mapping: Retrieves protein-coding Ensembl transcripts and maps InterPro domains and post-translational modifications onto canonical sequences.
• Isoform-Specific Analysis: Incorporates isoform-specific protein–protein interactions and binding regions from IntAct and links them to gene-set over-representation analysis.
• Technical Infrastructure: Employs Biopython, g:Profiler, MySQL-connector-python and FastAPI for back-end processing, and D3.js, jQuery, and DataTables for data presentation and visualization.

Scientific Applications:

• Cancer Genomics: Characterizes functional consequences of splice variants observed in cancer by linking DE transcripts to domain changes, PTMs, and interaction network alterations.
• Functional Annotation of Splice Variants: Identifies how alternative splicing events affect protein domains, modification sites, and isoform-specific interactions.
• Biomarker and Therapeutic Target Discovery: Supports identification of splice-variant–associated biomarkers and potential therapeutic targets through integrated enrichment and interaction analyses.

Methodology:

Integrates DE protein-coding transcript data; retrieves Ensembl transcripts; maps InterPro domains and post-translational modifications onto canonical sequences; incorporates isoform-specific protein–protein interactions and binding regions from IntAct; performs gene-set over-representation analysis via g:Profiler; and utilizes Biopython, MySQL-connector-python, FastAPI, D3.js, jQuery, and DataTables for computational processing and visualization.