Cascade

Cascade visualizes RNA-seq data from cancer genomics experiments in three-dimensional representations to integrate mutations, gene expression levels, and alternative splicing frequencies onto biological pathways for exploratory analysis.

Key Features:

• Integrated visualization: Simultaneous display and integration of mutations, gene expression levels, and alternative splicing frequencies derived from RNA-seq data.
• Biological pathway overlay: Overlay of experimental data onto known biological pathways, with support for predefined pathways and user-provided pathway definitions.
• Parameterized data selection via MySQL: Interaction with an underlying MySQL database to select data types and adjust parameters affecting which data are queried and visualized.
• 3D rendering: Use of three-dimensional visualization techniques to represent genomic measurements and their relationships.
• Scalability for cancer genomics datasets: Designed to handle large-scale datasets typical of cancer genomics projects and a wide range of genomic data types.

Scientific Applications:

• Cancer genomics data exploration: Comparative and integrative exploration of mutations, expression, and splicing from RNA-seq experiments in cancer studies.
• Pathway contextualization: Contextualizing RNA-seq–derived molecular changes within established biological pathways to aid interpretation.
• Hypothesis generation: Enabling generation of mechanistic hypotheses by integrating multiple genomic data modalities in a unified representation.

Methodology:

Three-dimensional visualization of RNA-seq data, overlay of experimental data onto biological pathways, and integration with a MySQL database to enable dynamic parameter and data-type selection.