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http://hdl.handle.net/10397/107007
Title: | Mem-ADSVM : a two-layer multi-label predictor for identifying multi-functional types of membrane proteins | Authors: | Wan, S Mak, MW Kung, SY |
Issue Date: | 7-Jun-2016 | Source: | Journal of theoretical biology, 7 June 2016, v. 398, p. 32-42 | Abstract: | Identifying membrane proteins and their multi-functional types is an indispensable yet challenging topic in proteomics and bioinformatics. However, most of the existing membrane-protein predictors have the following problems: (1) they do not predict whether a given protein is a membrane protein or not; (2) they are limited to predicting membrane proteins with single-label functional types but ignore those with multi-functional types; and (3) there is still much room for improvement for their performance. To address these problems, this paper proposes a two-layer multi-label predictor, namely Mem-ADSVM, which can identify membrane proteins (Layer I) and their multi-functional types (Layer II). Specifically, given a query protein, its associated gene ontology (GO) information is retrieved by searching a compact GO-term database with its homologous accession number. Subsequently, the GO information is classified by a binary support vector machine (SVM) classifier to determine whether it is a membrane protein or not. If yes, it will be further classified by a multi-label multi-class SVM classifier equipped with an adaptive-decision (AD) scheme to determine to which functional type(s) it belongs. Experimental results show that Mem-ADSVM significantly outperforms state-of-the-art predictors in terms of identifying both membrane proteins and their multi-functional types. This paper also suggests that the two-layer prediction architecture is better than the one-layer for prediction performance. For reader׳s convenience, the Mem-ADSVM server is available online at http://bioinfo.eie.polyu.edu.hk/MemADSVMServer/. | Keywords: | Adaptive-decision scheme Gene ontology Membrane protein type prediction Multi-label classification Two-layer classification |
Publisher: | Academic Press | Journal: | Journal of theoretical biology | ISSN: | 0022-5193 | EISSN: | 1095-8541 | DOI: | 10.1016/j.jtbi.2016.03.013 | Rights: | © 2016 Elsevier Ltd. All rights reserved. © 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/ The following publication Wan, S., Mak, M. W., & Kung, S. Y. (2016). Mem-ADSVM: A two-layer multi-label predictor for identifying multi-functional types of membrane proteins. Journal of theoretical biology, 398, 32-42 is available at https://doi.org/10.1016/j.jtbi.2016.03.013. |
Appears in Collections: | Journal/Magazine Article |
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Mak_Mem-Adsvm_Two-Layer_Multi-Label.pdf | Pre-Published version | 1.88 MB | Adobe PDF | View/Open |
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