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Network Biology, 2013, 3(1): 15-28
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Article

Changes in protein interaction networks between normal and cancer conditions: Total chaos or ordered disorder?

K. M. Taufiqur Rahman, Md. Fahmid Islam , Rajat Suvra Banik, Ummay Honi, Farhana Sharmin Diba, Sharmin Sultana Sumi, Shah Md. Tamim Kabir, Md. Shamim Akhter
Biotechnology and Genetic Engineering Discipline, Khulna University, Bangladesh

Received 15 November 2012;Accepted 18 December 2012;Published online 1 March 2013
IAEES

Abstract
New insights to understand the dynamics of enormous modifications during cancer in comparison to healthy condition have made the ground for the emergence of sophisticated systemic approaches like Network Systems Biology in the twenty first century which is potentially effective to model different biological phenomena such as regulation of gene-expression and protein-protein interaction. In the current study, the construction and computational analysis of protein interaction networks (PINs) based on expression data of proteins involved in 10 major cancer signal transduction pathways were done in case of five different tissues e.g. bone, breast, colon, kidney and liver for both normal and cancer conditions. Differential expression database GeneHubs-Gepis, and protein-protein interaction prediction tools PIPs and STRING were applied for primary data retrieval. Upregulation and downregulation of proteins in various cancers were analyzed to identify patterns in PINs during cancer signaling. Different network parameters were evaluated and comparisons were made among normal and cancer networks for each tissue and for different cancer based on Cytoscape software package. The networks for cancer show notable differences and fluctuations from normal ones for various network parameters. A cluster of 34 upregulated proteins with 76 relevant interactions was also found to be conserved in all five cancerous tissues.

Keywords cancer;network systems biology;signal transduction pathways;protein interaction network.

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