title: Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms.
abstract: BACKGROUND
  In the field of network science, exploring principal and crucial modules or communities is critical in the deduction of relationships and organization of complex networks. This approach expands an arena, and thus allows further study of biological functions in the field of network biology. As the clustering algorithms that are currently employed in finding modules have innate uncertainties, external and internal validations are necessary.
  
  
  METHODS
  Sequence and network structure alignment, has been used to define the Interlog Protein Network (IPN). This network is an evolutionarily conserved network with communal nodes and less false-positive links. In the current study, the IPN is employed as an evolution-based benchmark in the validation of the module finding methods. The clustering results of five algorithms; Markov Clustering (MCL), Restricted Neighborhood Search Clustering (RNSC), Cartographic Representation (CR), Laplacian Dynamics (LD) and Genetic Algorithm; to find communities in Protein-Protein Interaction networks (GAPPI) are assessed by IPN in four distinct Protein-Protein Interaction Networks (PPINs).
  
  
  RESULTS
  The MCL shows a more accurate algorithm based on this evolutionary benchmarking approach. Also, the biological relevance of proteins in the IPN modules generated by MCL is compatible with biological standard databases such as Gene Ontology, KEGG and Reactome.
  
  
  CONCLUSIONS
  In this study, the IPN shows its potential for validation of clustering algorithms due to its biological logic and straightforward implementation.
authors.affiliation: Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, 69 Pasteur St, PO Box 13164, Tehran, Iran. mjafari@ipm.ir.|School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Shahid Lavasani St, PO Box 19395-5746, Tehran, Iran. mjafari@ipm.ir.
authors.forename: Mohieddin
authors.initials: M
authors.lastname: Jafari
authors.affiliation: Department of Computational Biology, Faculty of High Technologies, Tarbiat Modares University, Jalal Ale Ahmad Highway, PO Box 14115-111, Tehran, Iran. mirzaie@ipm.ir.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mirzaie
authors.affiliation: National Institute of Genetic Engineering and Biotechnology (NIGEB), Pajoohesh Blvd, 17 Km Tehran-Karaj Highway, PO Box 161-14965, Tehran, Iran. sadeghi@nigeb.ac.ir.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Sadeghi
mesh_terms: D000465:Algorithms; D000818:Animals; D019985:Benchmarking; D005075:Biological Evolution; D016000:Cluster Analysis; D006801:Humans; D008390:Markov Chains; D008928:Mitochondria / Q000378:metabolism; D060066:Protein Interaction Maps; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*
chemical_list: D011506:Proteins