ISOexpresso: a web-based platform for isoform-level expression analysis in human cancer

Area of Science:

• Genomics
• Bioinformatics
• Cancer Research

Background:

• Alternative splicing produces multiple gene isoforms with varying functions.
• Aberrant alternative splicing is common in cancer, impacting tumor growth.
• No user-friendly, public platform exists for analyzing isoform expression in cancer.

Purpose of the Study:

• To develop ISOexpresso, a web-based platform for analyzing gene isoform expression and alterations in cancer.
• To provide tools for identifying tumor-specific isoforms and predicting mutation consequences.

Main Methods:

• Developed ISOexpresso with two core functions: Isoform Expression View and User Data Annotation.
• Isoform Expression View visualizes condition-specific RNA/isoform expression patterns.
• User Data Annotation prioritizes transcripts for mutation effect prediction based on expression levels.

Main Results:

• ISOexpresso allows identification of major isoforms and comparison with canonical isoforms.
• The platform facilitates discovery of potential tumor-specific isoforms.
• ISOexpresso successfully reproduced known isoform expression patterns in cancer.

Conclusions:

• ISOexpresso is a valuable, accessible resource for isoform expression analysis in cancer research.
• The platform aids in hypothesis generation and confirmation at the isoform level.
• ISOexpresso is available online at http://wiki.tgilab.org/ISOexpresso/.