APPEX

APPEX performs survival analysis to identify and validate prognostic molecular signatures that correlate with cancer patient outcomes.

Key Features:

• Versatile Statistical Methods: Implements workflows CoxSingle and CoxMulti (Cox proportional hazards), IntransSingle and IntransMulti (univariate and multivariate invariant marker detection), SuperPC (principal component analysis combined with survival data), TimeRoc (time-dependent ROC curves), and multivariate analysis for multi-variable evaluation.
• Extensive Dataset Repository: Hosts a repository of 236 publicly available datasets that have been collected, processed, and stored for independent validation of prognostic signatures.
• Case Studies for Validation: Includes case studies on disease recurrence and bladder cancer progression demonstrating application of workflow combinations.

Scientific Applications:

• Prognostic Marker Discovery: Identifies genes and other molecular features associated with cancer patient survival.
• Cross-cohort Validation: Validates prognostic markers across diverse public datasets to assess reproducibility.
• Characterization of Tumor Heterogeneity: Explores genetic and epigenetic alterations contributing to cancer heterogeneity and their associations with prognosis.

Methodology:

Computational methods include survival analysis using the Cox proportional hazards model (CoxSingle, CoxMulti), univariate and multivariate approaches (IntransSingle, IntransMulti), SuperPC (principal component analysis integrated with survival data), TimeRoc (time-dependent ROC analysis), and multivariate evaluation, applied to processed public datasets.