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

Chao Ren,Wenjie Shu,Gaole An,Xiaochen Bo,Zhangyi Ouyang,Chenghui Zhao

doi:10.1038/s41598-018-20232-4

Chao Ren, Wenjie Shu + Show 4 more

Open Access

https://doi.org/10.1038/s41598-018-20232-4

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Journal: Scientific Reports	Publication Date: Jan 30, 2018
Citations: 27	License type: open-access

Affiliation: Beijing Radiation Center

Abstract

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.

Highlights

Long noncoding RNAs, a class of noncoding RNAs with lengths exceeding 200 nucleotides, play a vital role in dysfunctional networks in cancer[1]
Evidence has suggested that long noncoding RNAs (lncRNAs) play a crucial role in cancer; the screening of candidate lncRNAs and definition of their function in specific cancers is still challenging
We present Lnc2Catlas, which compiles multiple quantitative assessments of the associations between lncRNAs and cancer to help researchers prioritize candidate lncRNAs

Summary

Introduction

Long noncoding RNAs (lncRNAs), a class of noncoding RNAs with lengths exceeding 200 nucleotides, play a vital role in dysfunctional networks in cancer[1]. Many databases compiling lncRNAs have been developed and provide abundant resources for exploring the function of lncRNAs. LncRNAdb provides comprehensive annotations of eukaryotic long non-coding RNAs10. Hon CC et al used FANTOM5 cap analysis of gene expression data to generate a reliable long non-coding RNA (lncRNA) dataset across 1,829 human samples[14]. We developed Lnc2Catlas to compile the underlying quantitative associations between lncRNAs and cancer using multiple methods and data sources. 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, https://portal.gdc.cancer.gov/). It contains 247,124 lncRNA-SNP pairs, over two millions lncRNA-protein interactions, and 6,902 co-expression clusters.

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