The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases

The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases

Abstract Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), availab...

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Autores principales: Haixiu Yang, Desi Shang, Yanjun Xu, Chunlong Zhang, Li Feng, Zeguo Sun, Xinrui Shi, Yunpeng Zhang, Junwei Han, Fei Su, Chunquan Li, Xia Li
Formato: article
Lenguaje:EN
Publicado: Nature Portfolio 2017
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Science
Q
Acceso en línea:https://doaj.org/article/63ac65181b7c4162a88fa8a0dfaf5f88
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spelling oai:doaj.org-article:63ac65181b7c4162a88fa8a0dfaf5f882021-12-02T16:07:44ZThe LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases10.1038/s41598-017-06897-32045-2322https://doaj.org/article/63ac65181b7c4162a88fa8a0dfaf5f882017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-06897-3https://doaj.org/toc/2045-2322Abstract Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/ , to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.Haixiu YangDesi ShangYanjun XuChunlong ZhangLi FengZeguo SunXinrui ShiYunpeng ZhangJunwei HanFei SuChunquan LiXia LiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-6 (2017)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Haixiu Yang
Desi Shang
Yanjun Xu
Chunlong Zhang
Li Feng
Zeguo Sun
Xinrui Shi
Yunpeng Zhang
Junwei Han
Fei Su
Chunquan Li
Xia Li
The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases
description Abstract Well characterized the connections among diseases, long non-coding RNAs (lncRNAs) and drugs are important for elucidating the key roles of lncRNAs in biological mechanisms in various biological states. In this study, we constructed a database called LNCmap (LncRNA Connectivity Map), available at http://www.bio-bigdata.com/LNCmap/ , to establish the correlations among diseases, physiological processes, and the action of small molecule therapeutics by attempting to describe all biological states in terms of lncRNA signatures. By reannotating the microarray data from the Connectivity Map database, the LNCmap obtained 237 lncRNA signatures of 5916 instances corresponding to 1262 small molecular drugs. We provided a user-friendly interface for the convenient browsing, retrieval and download of the database, including detailed information and the associations of drugs and corresponding affected lncRNAs. Additionally, we developed two enrichment analysis methods for users to identify candidate drugs for a particular disease by inputting the corresponding lncRNA expression profiles or an associated lncRNA list and then comparing them to the lncRNA signatures in our database. Overall, LNCmap could significantly improve our understanding of the biological roles of lncRNAs and provide a unique resource to reveal the connections among drugs, lncRNAs and diseases.
format article
author Haixiu Yang
Desi Shang
Yanjun Xu
Chunlong Zhang
Li Feng
Zeguo Sun
Xinrui Shi
Yunpeng Zhang
Junwei Han
Fei Su
Chunquan Li
Xia Li
author_facet Haixiu Yang
Desi Shang
Yanjun Xu
Chunlong Zhang
Li Feng
Zeguo Sun
Xinrui Shi
Yunpeng Zhang
Junwei Han
Fei Su
Chunquan Li
Xia Li
author_sort Haixiu Yang
title The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases
title_short The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases
title_full The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases
title_fullStr The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases
title_full_unstemmed The LncRNA Connectivity Map: Using LncRNA Signatures to Connect Small Molecules, LncRNAs, and Diseases
title_sort lncrna connectivity map: using lncrna signatures to connect small molecules, lncrnas, and diseases
publisher Nature Portfolio
publishDate 2017
url https://doaj.org/article/63ac65181b7c4162a88fa8a0dfaf5f88
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