GFICLEE

GFICLEE predicts novel members of biological pathways and protein complexes genome-wide by using tree-based phylogenetic profiling to infer common single and continuous loss (SCL) events.

Key Features:

• Tree-Based Phylogenetic Profiling: Utilizes phylogenetic trees to analyze evolutionary patterns across genomes and focus on inferring SCL events.
• High Predictive Performance: Demonstrates superior predictive accuracy compared to existing tree-based methods for identifying new pathway or complex members.
• Computational Efficiency: Provides high computational efficiency enabling genome-wide analyses on personal computers.
• Validation and Comparison: Validated using human pathways from three different databases and compared against current tree-based methods across 10 different scales of genome datasets.

Scientific Applications:

• Genome-wide gene function prediction: Identification of candidate genes as members of biological pathways and protein complexes across whole genomes.
• Systems biology: Integration of predicted pathway and complex membership into network and pathway analyses.
• Evolutionary and functional genomics: Investigation of gene loss patterns and their relationship to gene function evolution using SCL event inference.

Methodology:

Performs tree-based phylogenetic profiling on genome phylogenies to infer common single and continuous loss (SCL) events, and was validated using human pathways from three databases with comparisons across 10 dataset scales.