Revealing protein functions based on relationships of interacting proteins and GO terms

Journal of Biomedical Semantics

Kai Che¹  Zhen Tian¹  Maozu Guo¹  Xiaoyan Liu¹  Zhixia Teng² 

[1] Department of Computer Science and Engineering, Harbin Institute of Technology;Department of Information Management and Information System, Northeast Forestry University;

关键词: Protein function;    Interacting protein;    Gene ontology;    Directed network;   

DOI  :  10.1186/s13326-017-0139-8

来源: DOAJ

【 摘 要 】

Abstract Background In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. These methods supposed that two proteins share the same function if they interact with each other. However, it is reported by recent studies that the functions of two interacting proteins may be just related. It will mislead the prediction of protein function. Therefore, there is a need for investigating the functional relationship between interacting proteins. Results In this paper, the functional relationship between interacting proteins is studied and a novel method, called as GoDIN, is advanced to annotate functions of interacting proteins in Gene Ontology (GO) context. It is assumed that the functional difference between interacting proteins can be expressed by semantic difference between GO term and its relatives. Thus, the method uses GO term and its relatives to annotate the interacting proteins separately according to their functional roles in the PPI network. The method is validated by a series of experiments and compared with the concerned method. The experimental results confirm the assumption and suggest that GoDIN is effective on predicting functions of protein. Conclusions This study demonstrates that: (1) interacting proteins are not equal in the PPI network, and their function may be same or similar, or just related; (2) functional difference between interacting proteins can be measured by their degrees in the PPI network; (3) functional relationship between interacting proteins can be expressed by relationship between GO term and its relatives.

【 授权许可】

Unknown