ExonMiner: Web service for analysis of GeneChip Exon array data

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Splicing isoform-specific transcriptional regulations are linked to diseases.
• Detecting splice variations is crucial for understanding disease-specific transcriptional regulation.
• Affymetrix Human Exon 1.0 ST Array provides exon-level expression data for genome-wide analysis.

Purpose of the Study:

• To develop a comprehensive web service for analyzing exon array data.
• To detect transcripts with significantly different splicing patterns between cell types (e.g., normal vs. cancer).
• To identify exon-level biomarkers for diseases.

Main Methods:

• Developed ExonMiner, an all-in-one web service for exon array data analysis.
• Implemented data normalization, two-way ANOVA statistical analysis, and visualization (heatmaps, barplots).
• Utilized a supercomputer system for genome-wide analysis of over 300,000 transcripts.

Main Results:

• ExonMiner successfully identifies transcripts with significantly different splice patterns.
• The service enables efficient visualization and meta-analysis for biomarker detection.
• Genome-wide analysis revealed potential aberrant splice variations in cancer cells.

Conclusions:

• ExonMiner is a user-friendly, web-based tool requiring only internet browser access.
• It allows for rapid analysis of large exon array datasets within hours.
• The platform provides high-level statistical analysis to identify aberrant splice variants as biomarkers.