Long non-coding RNA Databases in Cardiovascular Research


The available data have been grouped into four categories: basic genomic annotation, lncRNA expression, molecular interactions, and sequence variants.

With rising interest in the regulatory functions of long non-coding RNAs (lncRNAs) in complex human diseases such as cardiovascular diseases, there is an increasing need in public databases offering comprehensive and integrative data for all aspects of these versatile molecules. Recently, a variety of public data repositories specialized in lncRNAs have been developed, which make use of huge high-throughput data particularly from next-generation sequencing (NGS) approaches.

Here, researchers from the University of Muenster, provide an overview of current lncRNA databases covering basic and functional annotation, lncRNA expression and regulation, interactions with other biomolecules, and genomic variants influencing the structure and function of lncRNAs.

The prominent lncRNA antisense noncoding RNA in the INK4 locus (ANRIL), which has been unequivocally associated with coronary artery disease through genome-wide association studies (GWAS), serves as an example to demonstrate the features of each individual database.

Database Weblink Data content
ChIPBase 1.1 http://deepbase.sysu.edu.cn/chipbase/ 543 ChIP-Seq datasets
C-It-Loci http://c-it-loci.uni-frankfurt.de/ 119 RNA-Seq datasets
Co-LncRNA http://www.bio-bigdata.com/Co-LncRNA/ 241 RNA-Seq datasets
DIANA-LncBase http://carolina.imis.athena-innovation.gr/index.php?r=lncbasev2 CLIP-validated and predicted miRNA targets on lncRNAs
GermlncRNA http://germlncrna.cbiit.cuhk.edu.hk/ Germ cell-related expression data
Linc2go http://www.bioinfo.tsinghua.edu.cn/∼liuke/Linc2GO/index.html Functional annotation of predicted RNA interactions
LincSNP 5000 lincRNAs and 140,000 disease-associated SNPs
lnCeDB http://gyanxet-beta.com/lncedb/ > 25,000 lncRNA transcripts from GENCODE
LNCipedia 3.1 http://www.lncipedia.org/ 111,685 lncRNA transcripts from literature and public databases
LncReg http://bioinformatics.ustc.edu.cn/lncreg/ 1081 manually-curated lncRNA interactions
lncRNA2Function http://mlg.hit.edu.cn/lncrna2function/ 9625 lncRNAs and RNA-Seq data from 19 tissues
LncRNA2Target http://mlg.hit.edu.cn/lncrna2target/ lncRNA−target association from knockdown/overexpression
lncRNAdb v2.0 http://lncrnadb.com/ 295 lncRNA genes curated from literature
LncRNADisease http://cmbi.bjmu.edu.cn/lncrnadisease > 1000 literature-extracted lncRNA−disease annotations
lncRNAMap http://lncrnamap.mbc.nctu.edu.tw/php/ RNA-Seq data from GEO and SRA
lncRNASNP http://bioinfo.life.hust.edu.cn/lncRNASNP/ Predicted effects of SNPs in >30,000 lncRNA transcripts
lncRNAtor http://lncrnator.ewha.ac.kr/index.htm 243 RNA-Seq studies from public databases
LncRNAWiki http://lncrna.big.ac.cn/index.php/Main_Page lncRNAs of GENCODE, NONCODE, LNCipedia, and lncRNAdb
lncRNome http://genome.igib.res.in/lncRNome/ > 17,000 lncRNAs from public databases
NONCODE 2016 http://www.noncode.org/ 527,336 lncRNA transcripts from literature and public databases
NPInter 3.0 http://www.bioinfo.org/NPInter/ about 500,000 validated molecular interactions
NRED http://nred.matticklab.com/cgi-bin/ncrnadb.pl Expression profiles from 8 microarray platforms
PhyloNONCODE http://www.bioinfo.org/phyloNoncode/ Conservation annotation for >135,000 lncRNAs
PLncDB http://chualab.rockefeller.edu/gbrowse2/homepage.html > 13,000 lncRNAs from tiling arrays and RNA-Seq
SNP@lincTFBS 5835 lincRNAs, 690 ChIP-Seq datasets, and 140,000 SNPs from dbSNP
starBase v2.0 http://starbase.sysu.edu.cn/ 111 CLIP-Seq datasets
TF2LncRNA http://mlg.hit.edu.cn/tf2lncrna/analyze.jsp 22,531 lncRNA transcripts and 425 ChIP-Seq datasets
zflncRNApedia http://genome.igib.res.in/zflncRNApedia/ ChIP-Seq and RNA-Seq data for 2267 zebrafish lncRNAs

Rühle F, Stoll M. (2016) Long non-coding RNA Databases in Cardiovascular Research. Genomics Proteomics Bioinformatics [Epub ahead of print]. [article]

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