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Online Journal of Bioinformatics ©
Volume 13(3):382-390, 2012.
K-shell decomposition based analysis of S. pombe protein networks
Praveen Kumar Singh1, Madhvi Shakya2
1Department of Bioinformatics and 2Mathematics, Maulana Azad National Institute of Technology Bhopal, India
Singh PK, Shakya M., K-shell decomposition based analysis of S. pombe protein networks, Online J Bioinform., 13(3):382-390, 2012. Understanding protein interaction networks requires a broad range of approaches and methods from the domains of biology, chemistry, physics, and mathematics. The fundamental challenge is to decipher the "protein interactome" associated with different protein functions and structures. This demands the acquisition and integration of vast amounts of data of many types, at multiple scales. Here a popular mathematical approach’’ k-shell Decomposition” has been used to understand protein interactome of modal organism S. pombe. K-shell decomposition is shown to be easy method to find the most effective and influential nodes (proteins) in huge complex networks. Here through k-shell decomposition method each node is assigned a specific k-shell and then k-shell based distribution of nodes is compared with known functions of proteins. Specific patterns of node distribution have been obtained with protein functions. Ribosomal proteins, backbone of proteome having highest k-shell index and found in central core. In the similar manner other proteins involved in translation, transcription, sorting and degradation found to be near to central core. Nodes involved in metabolic network found in outer k-shell with lower k-shell index.
Keywords: Protein interaction network, K-shell, protein functions, metabolic networks