Cancer DEIso

Cancer DEIso performs integrative analyses of gene- and isoform-level RNA-seq data to identify cancer-associated markers and assess stage-specific expression and survival associations using The Cancer Genome Atlas (TCGA) patient, sample sheet, clinical, and human genome datasets.

Key Features:

• Comprehensive Data Integration: Consolidates patient RNA-seq data, sample sheets, clinical information, and human genome datasets from The Cancer Genome Atlas (TCGA).
• Multi-Level Analysis: Supports gene-level and isoform-level analyses to investigate alternative splicing and transcript variant roles in carcinogenesis.
• Functional Search Tools: Enables searching for potential gene or isoform markers specific to cancer types and stages, identifying cancer types and stages associated with particular genes or isoforms, and performing expression survival analysis correlating gene/isoform expression with patient outcomes.
• Visualization Tools: Provides visualization for comparing gene- or isoform-level stage-specific expression patterns.

Scientific Applications:

• Isoform-level biomarker discovery: Identifies diagnostic markers that may be overlooked by gene-level expression analysis, including potential colorectal cancer isoform markers.
• Precision oncology support: Facilitates identification of novel biomarkers and therapeutic targets by integrating gene- and isoform-level expression with clinical and stage information for personalized medicine approaches.

Methodology:

The platform leverages patient RNA-seq data alongside clinical and genomic datasets from TCGA and processes them through an integrated analytical framework to perform survival analyses and stage-specific expression comparisons.