FunCoup

FunCoup predicts functional couplings between genes and gene products by integrating diverse experimental and statistical evidence to construct genome-wide networks of functional associations across eukaryotic species.

Key Features:

• Functional Coupling Classes: Categorizes functional couplings into participation in the same signaling cascade, involvement in the same metabolic process, co-membership within a protein complex, and physical interaction.
• Evidence Integration: Uses Bayesian integration to combine multiple types of experimental and statistical evidence for predicting couplings.
• Regularization Procedure: Applies a regularization procedure that automatically downweights redundant evidence.
• Phylogenetic Profile Similarity: Incorporates phylogenetic profile similarity as an evidence type to capture evolutionary conservation of functions.
• Genome-wide Network Construction: Constructs genome-wide networks of functional associations across eukaryotic species.
• Data Updates (FunCoup 3.0): Includes refreshed datasets and newly added data in version FunCoup 3.0.

Scientific Applications:

• Pathway and Metabolism Analysis: Investigate signaling pathways and metabolic networks through predicted functional associations.
• Protein Complex and Interaction Studies: Study protein complex membership and physical interactions among gene products.
• Evolutionary Functional Analysis: Explore evolutionary conservation and divergence in gene functions using phylogenetic profile similarity.
• Systems-level Cellular Mechanisms: Map higher-level mechanisms of cellular processes via genome-wide functional association networks.

Methodology:

Bayesian integration of multiple experimental and statistical evidence types, a regularization procedure to downweight redundant evidence, incorporation of phylogenetic profile similarity, and construction of genome-wide functional association networks.