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The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier
Abstract Motivation The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming ex...
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Published in: | Bioinformatics 2018-07, Vol.34 (13), p.2185-2194 |
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container_issue | 13 |
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container_title | Bioinformatics |
container_volume | 34 |
creator | Cao, Zhen Pan, Xiaoyong Yang, Yang Huang, Yan Shen, Hong-Bin |
description | Abstract
Motivation
The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming experiments for identifying subcellular localization of lncRNAs, computational methods are urgently desired. However, to the best of our knowledge, there are no computational tools for predicting the lncRNA subcellular locations to date.
Results
In this study, we report an ensemble classifier-based predictor, lncLocator, for predicting the lncRNA subcellular localizations. To fully exploit lncRNA sequence information, we adopt both k-mer features and high-level abstraction features generated by unsupervised deep models, and construct four classifiers by feeding these two types of features to support vector machine (SVM) and random forest (RF), respectively. Then we use a stacked ensemble strategy to combine the four classifiers and get the final prediction results. The current lncLocator can predict five subcellular localizations of lncRNAs, including cytoplasm, nucleus, cytosol, ribosome and exosome, and yield an overall accuracy of 0.59 on the constructed benchmark dataset.
Availability and implementation
The lncLocator is available at www.csbio.sjtu.edu.cn/bioinf/lncLocator.
Supplementary information
Supplementary data are available at Bioinformatics online. |
doi_str_mv | 10.1093/bioinformatics/bty085 |
format | article |
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Motivation
The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming experiments for identifying subcellular localization of lncRNAs, computational methods are urgently desired. However, to the best of our knowledge, there are no computational tools for predicting the lncRNA subcellular locations to date.
Results
In this study, we report an ensemble classifier-based predictor, lncLocator, for predicting the lncRNA subcellular localizations. To fully exploit lncRNA sequence information, we adopt both k-mer features and high-level abstraction features generated by unsupervised deep models, and construct four classifiers by feeding these two types of features to support vector machine (SVM) and random forest (RF), respectively. Then we use a stacked ensemble strategy to combine the four classifiers and get the final prediction results. The current lncLocator can predict five subcellular localizations of lncRNAs, including cytoplasm, nucleus, cytosol, ribosome and exosome, and yield an overall accuracy of 0.59 on the constructed benchmark dataset.
Availability and implementation
The lncLocator is available at www.csbio.sjtu.edu.cn/bioinf/lncLocator.
Supplementary information
Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/bty085</identifier><identifier>PMID: 29462250</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><ispartof>Bioinformatics, 2018-07, Vol.34 (13), p.2185-2194</ispartof><rights>The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c397t-bf72fd496b49e0b64bc90b032cd42d9548726c673c5df677b8d592bbf17c97ed3</citedby><cites>FETCH-LOGICAL-c397t-bf72fd496b49e0b64bc90b032cd42d9548726c673c5df677b8d592bbf17c97ed3</cites><orcidid>0000-0002-4029-3325</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,1604,27924,27925</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/bty085$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29462250$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Hancock, John</contributor><creatorcontrib>Cao, Zhen</creatorcontrib><creatorcontrib>Pan, Xiaoyong</creatorcontrib><creatorcontrib>Yang, Yang</creatorcontrib><creatorcontrib>Huang, Yan</creatorcontrib><creatorcontrib>Shen, Hong-Bin</creatorcontrib><title>The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Abstract
Motivation
The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming experiments for identifying subcellular localization of lncRNAs, computational methods are urgently desired. However, to the best of our knowledge, there are no computational tools for predicting the lncRNA subcellular locations to date.
Results
In this study, we report an ensemble classifier-based predictor, lncLocator, for predicting the lncRNA subcellular localizations. To fully exploit lncRNA sequence information, we adopt both k-mer features and high-level abstraction features generated by unsupervised deep models, and construct four classifiers by feeding these two types of features to support vector machine (SVM) and random forest (RF), respectively. Then we use a stacked ensemble strategy to combine the four classifiers and get the final prediction results. The current lncLocator can predict five subcellular localizations of lncRNAs, including cytoplasm, nucleus, cytosol, ribosome and exosome, and yield an overall accuracy of 0.59 on the constructed benchmark dataset.
Availability and implementation
The lncLocator is available at www.csbio.sjtu.edu.cn/bioinf/lncLocator.
Supplementary information
Supplementary data are available at Bioinformatics online.</description><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><recordid>eNqNkDtPwzAUhS0EoqXwE0AeWUIdx4ljtqriJVUgoTJHfoLBiYudDOXX4yoFiY3pPvzdc-QDwHmOrnLEirmw3nbGh5b3Vsa56LeoLg_ANCcVyjAq2WHqi4pmpEbFBJzE-I5QmRNCjsEEM1JhXKIp6NdvGrpOrrzkvQ_XkMM4CKmdGxwP0KW1s1_Jw3dwE7SyMlEw-aan7hV2vsukVza1z4-LCAWPWsHEJpmey4806C7qVjgNpeMxWmN1OAVHhruoz_Z1Bl5ub9bL-2z1dPewXKwyWTDaZ8JQbBRhlSBMI1ERIRkSqMBSEaxYSWqKK1nRQpbKVJSKWpUMC2FyKhnVqpiBy1F3E_znoGPftDbu_sY77YfYYIRonheUkYSWIyqDjzFo02yCbXnYNjlqdoE3fwNvxsDT3cXeYhCtVr9XPwknAI2AHzb_1PwG0guVEQ</recordid><startdate>20180701</startdate><enddate>20180701</enddate><creator>Cao, Zhen</creator><creator>Pan, Xiaoyong</creator><creator>Yang, Yang</creator><creator>Huang, Yan</creator><creator>Shen, Hong-Bin</creator><general>Oxford University Press</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4029-3325</orcidid></search><sort><creationdate>20180701</creationdate><title>The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier</title><author>Cao, Zhen ; Pan, Xiaoyong ; Yang, Yang ; Huang, Yan ; Shen, Hong-Bin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c397t-bf72fd496b49e0b64bc90b032cd42d9548726c673c5df677b8d592bbf17c97ed3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Cao, Zhen</creatorcontrib><creatorcontrib>Pan, Xiaoyong</creatorcontrib><creatorcontrib>Yang, Yang</creatorcontrib><creatorcontrib>Huang, Yan</creatorcontrib><creatorcontrib>Shen, Hong-Bin</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Cao, Zhen</au><au>Pan, Xiaoyong</au><au>Yang, Yang</au><au>Huang, Yan</au><au>Shen, Hong-Bin</au><au>Hancock, John</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2018-07-01</date><risdate>2018</risdate><volume>34</volume><issue>13</issue><spage>2185</spage><epage>2194</epage><pages>2185-2194</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><abstract>Abstract
Motivation
The long non-coding RNA (lncRNA) studies have been hot topics in the field of RNA biology. Recent studies have shown that their subcellular localizations carry important information for understanding their complex biological functions. Considering the costly and time-consuming experiments for identifying subcellular localization of lncRNAs, computational methods are urgently desired. However, to the best of our knowledge, there are no computational tools for predicting the lncRNA subcellular locations to date.
Results
In this study, we report an ensemble classifier-based predictor, lncLocator, for predicting the lncRNA subcellular localizations. To fully exploit lncRNA sequence information, we adopt both k-mer features and high-level abstraction features generated by unsupervised deep models, and construct four classifiers by feeding these two types of features to support vector machine (SVM) and random forest (RF), respectively. Then we use a stacked ensemble strategy to combine the four classifiers and get the final prediction results. The current lncLocator can predict five subcellular localizations of lncRNAs, including cytoplasm, nucleus, cytosol, ribosome and exosome, and yield an overall accuracy of 0.59 on the constructed benchmark dataset.
Availability and implementation
The lncLocator is available at www.csbio.sjtu.edu.cn/bioinf/lncLocator.
Supplementary information
Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>29462250</pmid><doi>10.1093/bioinformatics/bty085</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0002-4029-3325</orcidid><oa>free_for_read</oa></addata></record> |
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title | The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier |
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