shinySISPA

shinySISPA categorizes samples based on user-defined molecular profiles to identify sample groups that support specific gene-panel molecular profiles for clinical association analyses in multi-omics datasets.

Key Features:

• Gene panel data integration: Integrates gene expression levels and genetic variant data and supports the combination of multiple omics data types for analysis of gene panels.
• User-specified molecular profiles: Accepts user-defined profiles that can include combinations of mutations and associated gene expression changes.
• Sample group definition: Assigns samples into two groups—those that support the specified molecular profile and those that do not—to enable downstream comparative analyses.
• Implements SISPA method: Executes the Sample Integrated Set Profile Analysis (SISPA) approach to combine omics evidence around user-defined profiles.

Scientific Applications:

• Cancer research: Tests many samples against targeted gene panels to identify samples supporting mutation-expression profiles relevant to tumor biology.
• Clinical association discovery: Facilitates identification of associations between molecular profiles and patient outcomes to inform treatment stratification and personalized medicine.

Methodology:

Implements a previously published SISPA method that integrates various omics data types into a cohesive analysis framework and identifies and categorizes samples based on their support for user-defined molecular profiles.