Bioinformatics Advance Access published online on October 28, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti104
Bioinformatics © Oxford University Press 2004; all rights reserved
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1 Gordon Life Science Institute, San Diego, CA 92130, USA; Shanghai Jiaotong University, Biomedical Engineering, Shanghai 200030, China; Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin, China
* To whom correspondence should be addressed.
Motivation: Most of the existing methods in predicting protein subcellular location were used to deal with the cases limited within the scope from 2 to 5 localizations, and only a few of them can be effectively extended to cover the cases of 12-14 localizations. This is because the more the locations involved, the poorer the success rate would be. Besides, some proteins may occur in several different subcellular locations, i.e., bear the feature of "multiplex locations". So far there is no method that can be used to effectively treat the difficult multiplex location problem. The present study was initiated in an attempt to address (1) how to efficiently identify the localization of a query protein among many possible subcellular locations, and (2) how to deal with the case of multiplex locations. Results: By hybridizing gene ontology, functional domain, and pseudo amino acid composition approaches, a new method has been developed that can be used to predict subcellular localization of proteins with multiplex location feature. A global analysis of the proteins in budding yeast classified into 22 locations was performed by jackknife cross-validation with the new method. The overall success identification rate thus obtained is 70%. In contrast to this, the corresponding rates obtained by some other existing methods were only 13-14%, indicating that the new method is very powerful and promissing. Furthermore, predictions were made for the 4 proteins whose localizations could not be determined by experiments, as well as for the 236 proteins whose localizations in budding yeast were ambiguous according to experimental observations. However, according to our predicted results, many of these "ambiguous proteins" were found to have a same score and ranking for several different subcellular locations, implying that they may simultaneously exist, or move around, in these locations. This finding is intriguing because it reflects the dynamic feature of these proteins in a cell that may be associated with some special biological functions.
Revised October 13, 2004
Accepted October 18, 2004
Article
Predicting protein localization in budding yeast
2 Gordon Life Science Institute, San Diego, CA 92130, USA; Biomolecular Sciences Department, UMIST, P.O. Box 88, Manchester, M60 1QD, UK
Kuo-Chen Chou, E-mail: kchou{at}san.rr.com
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