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

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 htt...

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Bibliographic Details
Published in:Scientific reports 2017-07, Vol.7 (1), p.6655-6, Article 6655
Main Authors: Yang, Haixiu, Shang, Desi, Xu, Yanjun, Zhang, Chunlong, Feng, Li, Sun, Zeguo, Shi, Xinrui, Zhang, Yunpeng, Han, Junwei, Su, Fei, Li, Chunquan, Li, Xia
Format: Article
Language:English
Subjects:
38/39
631/114/129
631/154
Browsing
Databases, Nucleic Acid
Drug development
Drugs
Humanities and Social Sciences
Humans
Molecular Sequence Annotation
multidisciplinary
RNA, Long Noncoding - metabolism
RNA, Long Noncoding - physiology
Science
Science (multidisciplinary)
Sequence Analysis, RNA
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Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-017-06897-3