title: Functional characterization and topological modularity of molecular interaction networks.
abstract: BACKGROUND
  Analyzing interaction networks for functional characterization poses significant challenges arising from the noisy, incomplete, and generic nature of both the interaction data as well as functional annotation of molecules. Network-based methods focus on interacting molecules (pairs or sets) occurring in close proximity to infer functional associations.
  
  
  RESULTS
  In this paper we perform a formal comparative investigation of the relationship between functional coherence and topological proximity in networks. We investigate the problem of assessing the coherence of sets of biomolecules (or segments thereof) taking into account functional specificity as well as the distribution of functional attributes across entity groups. We also propose novel measures of topological proximity that are more robust to noisy and incomplete interaction data.
  
  
  CONCLUSIONS
  We derive the following results in this paper: (i) there exists strong correlation between functional similarity and topological proximity in various network abstractions, with domain interaction networks (DDIs) demonstrating higher correlation than protein interaction networks (PPIs); (ii) measures that quantify coherence among entire sets of proteins are superior to aggregates of known pair-wise measures; and (iii) random-walk based measures of topological proximity are better suited to existing interaction data. We validate our methods on diverse data, including experimentally and computationally derived PPIs and DDIs, as well as on sets of known biologically related groups of molecules.
authors.affiliation: Department of Computer Science, Purdue University, West Lafayette, IN, USA. jpandey@cs.purdue.edu
authors.forename: Jayesh
authors.initials: J
authors.lastname: Pandey
authors.forename: Mehmet
authors.initials: M
authors.lastname: Koyutürk
authors.forename: Ananth
authors.initials: A
authors.lastname: Grama
mesh_terms: D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*
chemical_list: D011506:Proteins; D020543:Proteome