Abstract
BackgroundIn 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.ResultsIn 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.ConclusionsThis 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.
Highlights
In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network
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 Gene Ontology (GO) term and its relatives
The results suggest that the majority of interacting proteins share the same or similar terms, which is consistent with basic assumptions of GO terms in the directed PPI network (GoDIN)
Summary
Numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. It is widely recognized that a protein performs functions according to its partners in proteinprotein interaction (PPI) network. This recognition has motivated the development of numerous network-based methods for predicting protein function. These methods are proposed on the principle of guilt-by-association (GBA), that is, the closer the two proteins are in the network the more similar are their functions [5]. These network-based methods can be roughly grouped into two major classes: direct annotation methods [6,7,8,9,10,11]
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