CAS-viewer: web-based tool for splicing-guided integrative analysis of multi-omics cancer data

Area of Science:

• Genomics
• Bioinformatics
• Cancer Research

Background:

• The Cancer Genome Atlas (TCGA) provides extensive multi-omics data for 33 cancer types, crucial for advancing cancer research.
• Alternative splicing (AS) plays a significant role in cancer development and its interaction with epigenetic factors.
• Existing tools for analyzing TCGA data are limited, often analyzing only one data type (e.g., transcriptomics) at a time.

Purpose of the Study:

• To develop a web-based tool for integrating and analyzing multi-omics data from TCGA, focusing on alternative splicing.
• To enable a comprehensive understanding of the genetic architecture of cancer risk and outcomes through AS-guided data integration.
• To facilitate the discovery of potential cancer biomarkers by linking AS patterns with clinical and molecular data.

Main Methods:

• Implementation of CAS-viewer, a web-based application for integrative analysis of cancer genome data based on alternative splicing.
• Leveraging multi-cancer omics data (transcriptomics, methylation, miRNAs, SNPs) from TCGA.
• Linking differential transcript expression ratios to methylation, miRNA, and splicing regulatory elements for 33 cancer types.

Main Results:

• CAS-viewer illustrates alternative mRNA splicing patterns alongside methylation, miRNA, and SNP data for 33 cancer types.
• The tool provides analysis capabilities to link AS patterns with clinical data, identifying transcripts associated with survival outcomes.
• Facilitates the visualization and potential discovery of biomarkers by integrating multi-omics data.

Conclusions:

• CAS-viewer is a web-based application for integrating multi-omics data driven by transcript isoforms across multiple cancer types.
• The tool aids in the visualization and discovery of potential cancer biomarkers.
• It enables a deeper understanding of cancer through the integration of diverse TCGA datasets.