iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.

Predicting protein subcellular localization is an important and difficult problem, particularly when query proteins may have the multiplex character, i.e., simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular location pr...

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Autores principales:	Kuo-Chen Chou, Zhi-Cheng Wu, Xuan Xiao
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c29f909b2e5d485590c60dbc01753473
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spelling	oai:doaj.org-article:c29f909b2e5d485590c60dbc017534732021-11-18T06:56:30ZiLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.1932-620310.1371/journal.pone.0018258https://doaj.org/article/c29f909b2e5d485590c60dbc017534732011-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21483473/?tool=EBIhttps://doaj.org/toc/1932-6203Predicting protein subcellular localization is an important and difficult problem, particularly when query proteins may have the multiplex character, i.e., simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular location predictor can only be used to deal with the single-location or "singleplex" proteins. Actually, multiple-location or "multiplex" proteins should not be ignored because they usually posses some unique biological functions worthy of our special notice. By introducing the "multi-labeled learning" and "accumulation-layer scale", a new predictor, called iLoc-Euk, has been developed that can be used to deal with the systems containing both singleplex and multiplex proteins. As a demonstration, the jackknife cross-validation was performed with iLoc-Euk on a benchmark dataset of eukaryotic proteins classified into the following 22 location sites: (1) acrosome, (2) cell membrane, (3) cell wall, (4) centriole, (5) chloroplast, (6) cyanelle, (7) cytoplasm, (8) cytoskeleton, (9) endoplasmic reticulum, (10) endosome, (11) extracellular, (12) Golgi apparatus, (13) hydrogenosome, (14) lysosome, (15) melanosome, (16) microsome (17) mitochondrion, (18) nucleus, (19) peroxisome, (20) spindle pole body, (21) synapse, and (22) vacuole, where none of proteins included has ≥25% pairwise sequence identity to any other in a same subset. The overall success rate thus obtained by iLoc-Euk was 79%, which is significantly higher than that by any of the existing predictors that also have the capacity to deal with such a complicated and stringent system. As a user-friendly web-server, iLoc-Euk is freely accessible to the public at the web-site http://icpr.jci.edu.cn/bioinfo/iLoc-Euk. It is anticipated that iLoc-Euk may become a useful bioinformatics tool for Molecular Cell Biology, Proteomics, System Biology, and Drug Development Also, its novel approach will further stimulate the development of predicting other protein attributes.Kuo-Chen ChouZhi-Cheng WuXuan XiaoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 3, p e18258 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kuo-Chen Chou Zhi-Cheng Wu Xuan Xiao iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.
description	Predicting protein subcellular localization is an important and difficult problem, particularly when query proteins may have the multiplex character, i.e., simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular location predictor can only be used to deal with the single-location or "singleplex" proteins. Actually, multiple-location or "multiplex" proteins should not be ignored because they usually posses some unique biological functions worthy of our special notice. By introducing the "multi-labeled learning" and "accumulation-layer scale", a new predictor, called iLoc-Euk, has been developed that can be used to deal with the systems containing both singleplex and multiplex proteins. As a demonstration, the jackknife cross-validation was performed with iLoc-Euk on a benchmark dataset of eukaryotic proteins classified into the following 22 location sites: (1) acrosome, (2) cell membrane, (3) cell wall, (4) centriole, (5) chloroplast, (6) cyanelle, (7) cytoplasm, (8) cytoskeleton, (9) endoplasmic reticulum, (10) endosome, (11) extracellular, (12) Golgi apparatus, (13) hydrogenosome, (14) lysosome, (15) melanosome, (16) microsome (17) mitochondrion, (18) nucleus, (19) peroxisome, (20) spindle pole body, (21) synapse, and (22) vacuole, where none of proteins included has ≥25% pairwise sequence identity to any other in a same subset. The overall success rate thus obtained by iLoc-Euk was 79%, which is significantly higher than that by any of the existing predictors that also have the capacity to deal with such a complicated and stringent system. As a user-friendly web-server, iLoc-Euk is freely accessible to the public at the web-site http://icpr.jci.edu.cn/bioinfo/iLoc-Euk. It is anticipated that iLoc-Euk may become a useful bioinformatics tool for Molecular Cell Biology, Proteomics, System Biology, and Drug Development Also, its novel approach will further stimulate the development of predicting other protein attributes.
format	article
author	Kuo-Chen Chou Zhi-Cheng Wu Xuan Xiao
author_facet	Kuo-Chen Chou Zhi-Cheng Wu Xuan Xiao
author_sort	Kuo-Chen Chou
title	iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.
title_short	iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.
title_full	iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.
title_fullStr	iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.
title_full_unstemmed	iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.
title_sort	iloc-euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/c29f909b2e5d485590c60dbc01753473
work_keys_str_mv	AT kuochenchou iloceukamultilabelclassifierforpredictingthesubcellularlocalizationofsingleplexandmultiplexeukaryoticproteins AT zhichengwu iloceukamultilabelclassifierforpredictingthesubcellularlocalizationofsingleplexandmultiplexeukaryoticproteins AT xuanxiao iloceukamultilabelclassifierforpredictingthesubcellularlocalizationofsingleplexandmultiplexeukaryoticproteins
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iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins.

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