CladeOScope

CladeOScope identifies functional interactions between human genes by detecting clade-specific co-evolutionary signals using phylogenetic profiling (PP).

Key Features:

• Clade-specific co-evolution analysis: Applies phylogenetic profiling to clade-specific subsets (e.g., primates, mammals) to reveal local co-evolution signals missed by whole-eukaryote analyses.
• Large-scale comparative dataset: Analyzes 1,028 genomes spanning 66 clades to map the distribution of co-evolutionary signals.
• Pathway-specific insights: Detects distinct co-evolution patterns in pathways such as the non-homologous end joining pathway and the UFM1 ubiquitin-like protein pathway.
• Modular co-evolution approach: Models functional relationships conserved within specific evolutionary branches rather than universally across all eukaryotes.
• Complementary signal integration: Demonstrates that co-evolutionary signals are dispersed among clades and can be combined to improve identification of functional interactions.

Scientific Applications:

• Functional genomics: Supports annotation and prediction of gene functions and interactions among human genes by leveraging clade-specific co-evolution.
• Pathway analysis: Provides evolutionary-informed analysis of biological pathways, revealing clade-specific patterns in pathways like non-homologous end joining and the UFM1 pathway.
• Evolutionary biology: Informs studies of the modular distribution of gene evolution and co-evolution across eukaryotic clades.

Methodology:

Performs phylogenetic profiling (PP) on clade-specific subsets of genomes (1,028 genomes across 66 clades), compares co-evolutionary signals across clades, and conducts pathway-focused analyses including non-homologous end joining and the UFM1 ubiquitin-like protein pathway.