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Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers

Lnc2Catlas (http://lnc2catlas.bioinfotech.org/) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class of functional noncoding RNAs with lengths over 200 nt and play a vital role in diverse biological processes. Increasing evidence shows that lncRNA dysfunction...

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Autores principales: Ren, Chao, An, Gaole, Zhao, Chenghui, Ouyang, Zhangyi, Bo, Xiaochen, Shu, Wenjie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789977/
https://www.ncbi.nlm.nih.gov/pubmed/29382910
http://dx.doi.org/10.1038/s41598-018-20232-4
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author Ren, Chao
An, Gaole
Zhao, Chenghui
Ouyang, Zhangyi
Bo, Xiaochen
Shu, Wenjie
author_facet Ren, Chao
An, Gaole
Zhao, Chenghui
Ouyang, Zhangyi
Bo, Xiaochen
Shu, Wenjie
author_sort Ren, Chao
collection PubMed
description Lnc2Catlas (http://lnc2catlas.bioinfotech.org/) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class of functional noncoding RNAs with lengths over 200 nt and play a vital role in diverse biological processes. Increasing evidence shows that lncRNA dysfunction is associated with many human cancers/diseases. It is therefore important to understand the underlying relationship between lncRNAs and cancers. To this end, we developed Lnc2Catlas to compile quantitative associations between lncRNAs and cancers using three computational methods, assessing secondary structure disruption, lncRNA-protein interactions, and co-expression networks. Lnc2Catlas was constructed based on 27,670 well-annotated lncRNAs, 31,749,216 SNPs, 1,473 cancer-associated proteins, and 10,539 expression profiles of 33 cancers from The Cancer Genome Atlas (TCGA). Lnc2Catlas contains 247,124 lncRNA-SNP pairs, over two millions lncRNA-protein interactions, and 6,902 co-expression clusters. We deposited Lnc2Catlas on Alibaba Cloud and developed interactive, mobile device-compatible, user-friendly interfaces to help users search and browse Lnc2Catlas with ultra-low latency. Lnc2Catlas can aid in the investigation of associations between lncRNAs and cancers and can provide candidate lncRNAs for further experimental validation. Lnc2Catlas will facilitate an understanding of the associations between lncRNAs and cancer and will help reveal the critical role of lncRNAs in cancer.
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spelling pubmed-57899772018-02-15 Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers Ren, Chao An, Gaole Zhao, Chenghui Ouyang, Zhangyi Bo, Xiaochen Shu, Wenjie Sci Rep Article Lnc2Catlas (http://lnc2catlas.bioinfotech.org/) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class of functional noncoding RNAs with lengths over 200 nt and play a vital role in diverse biological processes. Increasing evidence shows that lncRNA dysfunction is associated with many human cancers/diseases. It is therefore important to understand the underlying relationship between lncRNAs and cancers. To this end, we developed Lnc2Catlas to compile quantitative associations between lncRNAs and cancers using three computational methods, assessing secondary structure disruption, lncRNA-protein interactions, and co-expression networks. Lnc2Catlas was constructed based on 27,670 well-annotated lncRNAs, 31,749,216 SNPs, 1,473 cancer-associated proteins, and 10,539 expression profiles of 33 cancers from The Cancer Genome Atlas (TCGA). Lnc2Catlas contains 247,124 lncRNA-SNP pairs, over two millions lncRNA-protein interactions, and 6,902 co-expression clusters. We deposited Lnc2Catlas on Alibaba Cloud and developed interactive, mobile device-compatible, user-friendly interfaces to help users search and browse Lnc2Catlas with ultra-low latency. Lnc2Catlas can aid in the investigation of associations between lncRNAs and cancers and can provide candidate lncRNAs for further experimental validation. Lnc2Catlas will facilitate an understanding of the associations between lncRNAs and cancer and will help reveal the critical role of lncRNAs in cancer. Nature Publishing Group UK 2018-01-30 /pmc/articles/PMC5789977/ /pubmed/29382910 http://dx.doi.org/10.1038/s41598-018-20232-4 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Ren, Chao
An, Gaole
Zhao, Chenghui
Ouyang, Zhangyi
Bo, Xiaochen
Shu, Wenjie
Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers
title Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers
title_full Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers
title_fullStr Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers
title_full_unstemmed Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers
title_short Lnc2Catlas: an atlas of long noncoding RNAs associated with risk of cancers
title_sort lnc2catlas: an atlas of long noncoding rnas associated with risk of cancers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789977/
https://www.ncbi.nlm.nih.gov/pubmed/29382910
http://dx.doi.org/10.1038/s41598-018-20232-4
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