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Mining Proteins Associated with Oral Squamous Cell Carcinoma in Complex Networks

  • Liu, Ying (State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University) ;
  • Liu, Chuan-Xia (State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University) ;
  • Wu, Zhong-Ting (State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University) ;
  • Ge, Lin (State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University) ;
  • Zhou, Hong-Mei (Department of Oral Medicine, West China School of Stomatology, Sichuan University)
  • Published : 2013.08.30

Abstract

The purpose of this study was to construct a protein-protein interaction (PPI) network related to oral squamous cell carcinoma (OSCC). Each protein was ranked and those most associated with OSCC were mined within the network. First, OSCC-related genes were retrieved from the Online Mendelian Inheritance in Man (OMIM) database. Then they were mapped to their protein identifiers and a seed set of proteins was built. The seed proteins were expanded using the nearest neighbor expansion method to construct a PPI network through the Online Predicated Human Interaction Database (OPHID). The network was verified to be statistically significant, the score of each protein was evaluated by algorithm, then the OSCC-related proteins were ranked. 38 OSCC related seed proteins were expanded to 750 protein pairs. A protein-protein interaction nerwork was then constructed and the 30 top-ranked proteins listed. The four highest-scoring seed proteins were SMAD4, CTNNB1, HRAS, NOTCH1, and four non-seed proteins P53, EP300, SMAD3, SRC were mined using the nearest neighbor expansion method. The methods shown here may facilitate the discovery of important OSCC proteins and guide medical researchers in further pertinent studies.

Keywords

Protein-protein interaction;nearest neighbor expansion;oral squamous cell carcinoma

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