Application of gap-constraints given sequential frequent pattern mining for protein function prediction.
OBJECTIVE
Predicting protein function from the protein-protein interaction network is challenging due to its complexity and huge scale of protein interaction process along with inconsistent pattern. Previously proposed methods such as neighbor counting, network analysis, and graph pattern mining has predicted functions by calculating the rules and probability of patterns inside network. Although these methods have shown good prediction, difficulty still exists in searching several functions that are exceptional from simple rules and patterns as a result of not considering the inconsistent aspect of the interaction network.


METHODS
In this article, we propose a novel approach using the sequential pattern mining method with gap-constraints. To overcome the inconsistency problem, we suggest frequent functional patterns to include every possible functional sequence-including patterns for which search is limited by the structure of connection or level of neighborhood layer. We also constructed a tree-graph with the most crucial interaction information of the target protein, and generated candidate sets to assign by sequential pattern mining allowing gaps.


RESULTS
The parameters of pattern length, maximum gaps, and minimum support were given to find the best setting for the most accurate prediction. The highest accuracy rate was 0.972, which showed better results than the simple neighbor counting approach and link-based approach.


CONCLUSIONS
The results comparison with other approaches has confirmed that the proposed approach could reach more function candidates that previous methods could not obtain.
Database/Bioinformatics Laboratory, College of Electrical and Computer Engineering Chungbuk National University, Cheongju, Korea.
Hyeon Ah
HA
Park
Syntekabio Incorporated, Korea Institute of Science and Technology, Seoul, Korea.
Taewook
T
Kim
Database/Bioinformatics Laboratory, College of Electrical and Computer Engineering Chungbuk National University, Cheongju, Korea.
Meijing
M
Li
Graduate School of Health Science Business Convergence, Chungbuk National University, Cheongju, Korea.
Ho Sun
HS
Shon
Medical Informatics∙Engineering, Korea National University of Transportation, Cheongju, Korea.
Jeong Seok
JS
Park
Database/Bioinformatics Laboratory, College of Electrical and Computer Engineering Chungbuk National University, Cheongju, Korea.
Keun Ho
KH
Ryu
frequent pattern mining with gap-constraint; graph pattern mining; protein function prediction; protein–protein interaction network; sequential pattern mining