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LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs

We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, w...

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Autores principales: Ning, Shangwei, Yue, Ming, Wang, Peng, Liu, Yue, Zhi, Hui, Zhang, Yan, Zhang, Jizhou, Gao, Yue, Guo, Maoni, Zhou, Dianshuang, Li, Xin, Li, Xia
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210641/
https://www.ncbi.nlm.nih.gov/pubmed/27924020
http://dx.doi.org/10.1093/nar/gkw945
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author Ning, Shangwei
Yue, Ming
Wang, Peng
Liu, Yue
Zhi, Hui
Zhang, Yan
Zhang, Jizhou
Gao, Yue
Guo, Maoni
Zhou, Dianshuang
Li, Xin
Li, Xia
author_facet Ning, Shangwei
Yue, Ming
Wang, Peng
Liu, Yue
Zhi, Hui
Zhang, Yan
Zhang, Jizhou
Gao, Yue
Guo, Maoni
Zhou, Dianshuang
Li, Xin
Li, Xia
author_sort Ning, Shangwei
collection PubMed
description We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations. Furthermore, we developed three flexible online tools to retrieve and analyze the data. Linc-Mart is a convenient way for users to customize their own data. Linc-Browse is a tool for all data visualization. Linc-Score predicts the associations between lncRNA and disease. In addition, we provided users a newly designed, user-friendly interface to search and download all the data in LincSNP 2.0 and we also provided an interface to submit novel data into the database. LincSNP 2.0 is a continually updated database and will serve as an important resource for investigating the functions and mechanisms of lncRNAs in human diseases.
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spelling pubmed-52106412017-01-05 LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs Ning, Shangwei Yue, Ming Wang, Peng Liu, Yue Zhi, Hui Zhang, Yan Zhang, Jizhou Gao, Yue Guo, Maoni Zhou, Dianshuang Li, Xin Li, Xia Nucleic Acids Res Database Issue We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations. Furthermore, we developed three flexible online tools to retrieve and analyze the data. Linc-Mart is a convenient way for users to customize their own data. Linc-Browse is a tool for all data visualization. Linc-Score predicts the associations between lncRNA and disease. In addition, we provided users a newly designed, user-friendly interface to search and download all the data in LincSNP 2.0 and we also provided an interface to submit novel data into the database. LincSNP 2.0 is a continually updated database and will serve as an important resource for investigating the functions and mechanisms of lncRNAs in human diseases. Oxford University Press 2017-01-04 2016-10-23 /pmc/articles/PMC5210641/ /pubmed/27924020 http://dx.doi.org/10.1093/nar/gkw945 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Ning, Shangwei
Yue, Ming
Wang, Peng
Liu, Yue
Zhi, Hui
Zhang, Yan
Zhang, Jizhou
Gao, Yue
Guo, Maoni
Zhou, Dianshuang
Li, Xin
Li, Xia
LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs
title LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs
title_full LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs
title_fullStr LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs
title_full_unstemmed LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs
title_short LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs
title_sort lincsnp 2.0: an updated database for linking disease-associated snps to human long non-coding rnas and their tfbss
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210641/
https://www.ncbi.nlm.nih.gov/pubmed/27924020
http://dx.doi.org/10.1093/nar/gkw945
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