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A Multi-Label Classifier for Predicting the Subcellular Localization of Gram-Negative Bacterial Proteins with Both Single and Multiple Sites

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  • Xuan Xiao
  • Zhi-Cheng Wu
  • Kuo-Chen Chou

Abstract

Prediction of protein subcellular localization is a challenging problem, particularly when the system concerned contains both singleplex and multiplex proteins. In this paper, by introducing the “multi-label scale” and hybridizing the information of gene ontology with the sequential evolution information, a novel predictor called iLoc-Gneg is developed for predicting the subcellular localization of Gram-positive bacterial proteins with both single-location and multiple-location sites. For facilitating comparison, the same stringent benchmark dataset used to estimate the accuracy of Gneg-mPLoc was adopted to demonstrate the power of iLoc-Gneg. The dataset contains 1,392 Gram-negative bacterial proteins classified into the following eight locations: (1) cytoplasm, (2) extracellular, (3) fimbrium, (4) flagellum, (5) inner membrane, (6) nucleoid, (7) outer membrane, and (8) periplasm. Of the 1,392 proteins, 1,328 are each with only one subcellular location and the other 64 are each with two subcellular locations, but none of the proteins included has pairwise sequence identity to any other in a same subset (subcellular location). It was observed that the overall success rate by jackknife test on such a stringent benchmark dataset by iLoc-Gneg was over 91%, which is about 6% higher than that by Gneg-mPLoc. As a user-friendly web-server, iLoc-Gneg is freely accessible to the public at http://icpr.jci.edu.cn/bioinfo/iLoc-Gneg. Meanwhile, a step-by-step guide is provided on how to use the web-server to get the desired results. Furthermore, for the user's convenience, the iLoc-Gneg web-server also has the function to accept the batch job submission, which is not available in the existing version of Gneg-mPLoc web-server. It is anticipated that iLoc-Gneg may become a useful high throughput tool for Molecular Cell Biology, Proteomics, System Biology, and Drug Development.

Suggested Citation

  • Xuan Xiao & Zhi-Cheng Wu & Kuo-Chen Chou, 2011. "A Multi-Label Classifier for Predicting the Subcellular Localization of Gram-Negative Bacterial Proteins with Both Single and Multiple Sites," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-10, June.
    • Handle: RePEc:plo:pone00:0020592
    DOI: 10.1371/journal.pone.0020592
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    References listed on IDEAS

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    1. Kuo-Chen Chou & Hong-Bin Shen, 2010. "Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization," PLOS ONE, Public Library of Science, vol. 5(6), pages 1-11, June.
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    1. Le-Le Hu & Tao Huang & Yu-Dong Cai & Kuo-Chen Chou, 2011. "Prediction of Body Fluids where Proteins are Secreted into Based on Protein Interaction Network," PLOS ONE, Public Library of Science, vol. 6(7), pages 1-8, July.
    2. Bi-Qing Li & Le-Le Hu & Lei Chen & Kai-Yan Feng & Yu-Dong Cai & Kuo-Chen Chou, 2012. "Prediction of Protein Domain with mRMR Feature Selection and Analysis," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-14, June.
    3. Tao Huang & Lei Chen & Yu-Dong Cai & Kuo-Chen Chou, 2011. "Classification and Analysis of Regulatory Pathways Using Graph Property, Biochemical and Physicochemical Property, and Functional Property," PLOS ONE, Public Library of Science, vol. 6(9), pages 1-11, September.
    4. Xiao Wang & Guo-Zheng Li, 2012. "A Multi-Label Predictor for Identifying the Subcellular Locations of Singleplex and Multiplex Eukaryotic Proteins," PLOS ONE, Public Library of Science, vol. 7(5), pages 1-9, May.
    5. Wu Zhu & Jian-an Fang & Yang Tang & Wenbing Zhang & Wei Du, 2012. "Digital IIR Filters Design Using Differential Evolution Algorithm with a Controllable Probabilistic Population Size," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-9, July.

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