tspair

tspair identifies top scoring pairs of genes whose relative expression rankings classify samples into two predefined groups using rank-based comparison of gene expression data.

Key Features:

• Simplicity and Interpretability: Classifiers use only two genes, enabling straightforward biological interpretation and facilitating development of assays such as PCR-based tests.
• Robustness to Technical Variations: Rank-based classification uses relative gene rankings rather than absolute expression, reducing sensitivity to normalization and other technical variation.
• Optimization of Sensitivity and Specificity: Identifies gene pairs that maximize the average of sensitivity and specificity across rank-based classifiers to assess candidate TSP classifiers.

Scientific Applications:

• Disease Diagnosis: Identifies gene pairs that distinguish diseased and healthy states for potential diagnostic tests.
• Biomarker Discovery: Pinpoints gene pairs with differential relative rankings across conditions to serve as biomarkers.
• Personalized Medicine: Produces classifiers that stratify individuals based on gene expression profiles to inform treatment decisions.

Methodology:

Calculates pairs of genes whose relative rankings exhibit the maximum difference between two predefined groups and evaluates rank-based classifiers by optimizing the average of sensitivity and specificity to select top-scoring pairs.