GeneSelector

GeneSelector identifies genes that are consistently ranked as differentially expressed across multiple statistical procedures to improve the stability and reproducibility of ranked gene lists.

Key Features:

• Consistent Gene Selection: Identifies genes that appear at the top of multiple ranked lists derived from different statistical analyses.
• Stability Assessment: Evaluates stability by generating perturbed datasets via leaving out samples, swapping class labels, generating bootstrap replicates, and adding noise.
• Aggregation Methods: Synthesizes multiple ranked lists using aggregation methods to produce a consolidated, stable gene ranking.

Scientific Applications:

• Differential expression analysis: Prioritizes genes that are reproducibly identified as differentially expressed across analysis methods.
• Ranked-list stability assessment: Quantifies the robustness of ranked gene lists under sample perturbations and label modifications.
• Biomarker selection for clinical applications: Aids selection of reproducible candidate biomarkers for downstream validation and potential clinical application.

Methodology:

Computational steps include identifying top-ranked genes across multiple lists, generating perturbed datasets by leaving out samples, swapping class labels, producing bootstrap replicates and adding noise, and aggregating ranked lists using aggregation methods.