Self-organizing maps in mining gene expression data
Information Sciences: an International Journal
Probabilistic models of information retrieval based on measuring the divergence from randomness
ACM Transactions on Information Systems (TOIS)
Using functional annotation to improve clusterings of gene expression patterns
Information Sciences—Informatics and Computer Science: An International Journal - Bioinformatics-selected papers from 4th CBGI & 6th JCIS Proceedings
A frequency-based and a poisson-based definition of the probability of being informative
Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval
The MIPS mammalian protein--protein interaction database
Bioinformatics
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Random walk biclustering for microarray data
Information Sciences: an International Journal
Clustering high dimensional data: A graph-based relaxed optimization approach
Information Sciences: an International Journal
Immune K-means and negative selection algorithms for data analysis
Information Sciences: an International Journal
Integrating induction and deduction for noisy data mining
Information Sciences: an International Journal
Information Sciences: an International Journal
A compact hybrid feature vector for an accurate secondary structure prediction
Information Sciences: an International Journal
Domain information based prediction of protein-protein interactions of glucosinolate biosynthesis
International Journal of Computer Applications in Technology
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Protein-protein interaction (PPI) networks play an outstanding role in the organization of life. Parallel to the growth of experimental techniques on determining PPIs, the emergence of computational methods has greatly accelerated the time needed for the identification of PPIs on a wide genomic scale. Although experimental approaches have limitations that can be complemented by the computational methods, the results from computational methods still suffer from high false positive rates which contribute to the lack of solid PPI information. Our study introduces the PPI-Filter; a computational framework aimed at improving PPI prediction results. It is a post-prediction process which involves filtration, using information based on three different genomic features; (i) gene ontology annotation (GOA), (ii) homologous interactions and (iii) protein families (PFAM) domain interactions. In the study, we incorporated a protein function prediction method, based on interacting domain patterns, the protein function predictor or PFP (), for the purpose of aiding the GOA. The goal is to improve the robustness of predicted PPI pairs by removing the false positive pairs and sustaining as much true positive pairs as possible, thus achieving a high confidence level of PPI datasets. The PPI-Filter has been proven to be applicable based on the satisfactory results obtained using signal-to-noise ratio (SNR) and strength measurements that were applied on different computational PPI prediction methods.