PhenoGeneRanker

PhenoGeneRanker prioritizes genes and phenotypes by utilizing multiplex heterogeneous gene-phenotype networks with multi-layer network support and empirical p-value calculation via random stratified sampling based on connectivity degree.

Key Features:

• Multiplex Heterogeneous Network Analysis: Utilizes multiplex heterogeneous gene-phenotype networks for prioritization.
• Multi-Layer Network Support: Allows construction and analysis of multi-layer gene and phenotype networks.
• Empirical P-Value Calculation: Calculates empirical p-values of gene and phenotype ranking using random stratified sampling based on connectivity degree in the network.

Scientific Applications:

• Gene Prioritization: Ranks candidate genes based on their network properties within heterogeneous gene-phenotype networks.
• Phenotype Prioritization: Ranks phenotypes based on their connectivity patterns in multi-layer network structures.

Methodology:

PhenoGeneRanker employs random stratified sampling of genes and phenotypes based on their connectivity degree in the network to calculate empirical p-values for ranking.