Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction.

ABSTRACT: The expansion of protein-ligand annotation databases has enabled large-scale networking of proteins by ligand similarity. These ligand-based protein networks, which implicitly predict the ability of neighboring proteins to bind related ligands, may complement biologically-oriented gene networks, which are used to predict functional or disease relevance. To quantify the degree to which such ligand-based protein associations might complement functional genomic associations, including sequence similarity, physical protein-protein interactions, co-expression, and disease gene annotations, we calculated a network based on the Similarity Ensemble Approach (SEA: sea.docking.org), where protein neighbors reflect the similarity of their ligands. We also measured the similarity with functional genom

SUBMITTER: O'Meara MJ 

PROVIDER: S-EPMC4965129 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature