ProLoc-rGO: Using rule-based knowledge with gene ontology terms for prediction of protein subnuclear localization

Wen Lin Huang*, Chun Wei Tung, Shih Wen Ho, Shinn-Ying Ho

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

Gene Ontology (GO) annotation is a controlled vocabulary of terms and phrases describing the function of genes and gene products, which has been succeeded in predicting subcellualr and subnuclear localization. Generally, each gene product is annotated by very few GO terms from more than 25,000 annotations available at present. How to represent a protein sequence using GO terms as features plays an important role in designing prediction systems for protein subnuclear localization. Our previous work ProLoc-GO can select a small number m out of a large number n GO terms, where m ≤≤ n. However, its off-line time for training is large up to several days even though running on high speedily PC clusters. Therefore, this study proposes an efficient system (ProLoc-rGO) by using the decision tree method to speedily mine m informative GO terms and acquire interpretable rule-based knowledge for predicting subnuclear localization. The ProLoc-rGO performing on SNL9-80 (714 proteins in nine compartments with ≤80 identity) can mine m=17 informative GO terms, 17 interpretable rules and yield training and test accuracies of 84.9% and 78.2%. For comparison, an accuracy 82.6% (Matthews correlation coefficient (MCC) = 0.711) for ProLoc-rGO performed on SNL9-80 (714 proteins in nine compartments with ≤80 identity) is obtained, which is better than 67.4% (MCC = 0.50) for Nuc-PLoc that fuses the pseudo-amino acid composition of a protein and its position-specific scoring matrix.

Original languageEnglish
Title of host publication2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '08
Pages201-206
Number of pages6
DOIs
StatePublished - 1 Dec 2008
Event2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '08 - Sun Valley, ID, United States
Duration: 15 Sep 200817 Sep 2008

Publication series

Name2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '08

Conference

Conference2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '08
CountryUnited States
CitySun Valley, ID
Period15/09/0817/09/08

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    Huang, W. L., Tung, C. W., Ho, S. W., & Ho, S-Y. (2008). ProLoc-rGO: Using rule-based knowledge with gene ontology terms for prediction of protein subnuclear localization. In 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '08 (pp. 201-206). [4675779] (2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB '08). https://doi.org/10.1109/CIBCB.2008.4675779