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Created on: 04-Mar-2014   Last updated on: 04-Mar-2014 |  How to cite this?
A compilation of Long non-coding RNA resources
Sirisha N. and Swetha Cheena (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources

Important features / utilities*CitationsYear of publicationRank by usage frequency Add comments
Rfam
http://rfam.sanger.ac.uk
Finds RNA families related to the sequence of coding or non-coding RNAs, which are provided as a query.
Griffiths-Jones, Sam, et al. "Rfam: annotating non-coding RNAs in complete genomes." Nucleic acids research 33.suppl 1 (2005): D121-D124 Pubmed PMID: 15608160 Pubmed Central PMCID: PMC540035 .
2005
21
lncRNAdb
http://www.lncrnadb.org
Resource on lncRNA annotations, sequence, structural information and their interactions with other genomic elements.
Amaral, Paulo P., et al. "lncRNAdb: a reference database for long noncoding RNAs." Nucleic acids research 39.suppl 1 (2011): D146-D151 Pubmed PMID: 21112873 Pubmed Central PMCID: PMC3013714.
2011
56
FRNAdb 3.0 - Functional RNA database
http://www.ncrna.org/frnadb
Provides sequences and functions of the noncoding RNA in different organisms.
Mituyama, Toutai, et al. "The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs." Nucleic acids research 37.suppl 1 (2009): D89-D92 Pubmed PMID: 18948287 Pubmed Central PMCID: PMC2686472.
2009
74
NONCODEv4 / NONCODEv3
http://www.noncode.org
Useful to identify the lncRNAs based on RNA-seq data, ID convertion from RefSeq or ENSEMBL ID to NONCODE ID.
NONCODEv4: exploring the world of long non-coding RNA genes Nucl. Acids Res. (1 January 2014) 42 (D1): D98-D103 PPMID: 24285305, NONCODE v3.0:Integrative annotation of long noncoding RNAs Nucleic Acids Res. 2012 Jan;40(Database issue):D210-5. Epub 2011 Dec 1 Pubmed PMID: 22135294 Pubmed Central PMCID: PMC3245065.
2014
76
NRED- nc rna expression database
http://nred.matticklab.com/cgi-bin/ncrnadb.pl
Provides integrated information about the annotated expression data from various sources.
Dinger, Marcel E., et al. "NRED: a database of long noncoding RNA expression." Nucleic acids research 37.suppl 1 (2009): D122-D126 Pubmed PMID: 18829717 Pubmed Central PMCID: PMC2686506.
2009
84
LNCipedia
http://www.lncipedia.org
Curated database on human annotated lincRNAs and provides information about transcript, gene and secondary structure, protein coding potential and miRNA binding information.
Volders, Pieter-Jan, et al. "LNCipedia: a database for annotated human lncRNA transcript sequences and structures." Nucleic acids research 41.D1 (2013): D246-D251 Pubmed PMID: 23042674 Pubmed Central PMCID: PMC3531107.
2013
89
LncRNADisease - The LncRNA and Disease Database
http://202.38.126.151/hmdd/html/tools/lncrnadisease.html
Provides information about lncRNA, its interactions with proteins, RNA, miRNA, DNA and its association in disease conditions.
Chen, Geng, et al. "LncRNADisease: a database for long-non-coding RNA-associated diseases." Nucleic acids research 41.D1 (2013): D983-D986 pubmed PMID: 23175614 Pubmed Central PMCID: PMC3531173.
2013
92
HGNC - HUGO Gene Nomenclature Committee
http://www.genenames.org/rna/LNCRNA
Provides comprehensive annotations of eukaryotic lncRNAs, which is taken from lncRNAdb.
-
2013
93
ChIPBase
http://deepbase.sysu.edu.cn/chipbase
Comprehensive resource for annotational and transcriptional regulatory relationships of ncRNAs.
Yang, Jian-Hua, et al. "ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data." Nucleic acids research 41.D1 (2013): D177-D187 Pubmed PMID: 23161675 Pubmed Central PMCID: PMC3531181.
2013
95
ncRNAimprint
http://rnaqueen.sysu.edu.cn/ncRNAimprint
-
Zhang, Ying, et al. "ncRNAimprint: a comprehensive database of mammalian imprinted noncoding RNAs." Rna 16.10 (2010): 1889-1901 Pubmed PMID: 20801769 Pubmed Central PMCID: PMC2941098.
2010
95
DIANA-LncBase
www.microrna.gr/LncBase
Provides information about miRNA and lncRNA interactions in human and mouse.
Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas TM, Hatzigeorgiou AG. DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucl. Acids Res. (2013) 41 (D1) Pubmed PMID: 23193281 Pubmed Central PMCID: PMC3531175
2013
96
iSeeRNA
http://sunlab.lihs.cuhk.edu.hk/iSeeRNA
It identifies coding and nc-RNAs from transcriptome sequencing data.
Sun, Kun, et al. "iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data." BMC genomics 14.Suppl 2 (2013): S7 Pubmed PMID: 23445546 Pubmed Central PMCID: PMC3582448.
2013
97
NPInter
http://www.bioinfo.org/NPInter
Provides information about interactions between ncRNA and other biomolecules.
Yuan, Jiao, et al. "NPInter v2. 0: an updated database of ncRNA interactions." Nucleic acids research 42.D1 (2014): D104-D108 Pubmed PMID: 24217916.
2014
97
starBase v2.0
http://starbase.sysu.edu.cn/index.php
Provides information about interactions between ncRNAs and, also ncRNA and protein.
Li, Jun-Hao, et al. "starBase v2. 0: decoding miRNA-ceRNA, miRNA-ncRNA and protein RNA interaction networks from large-scale CLIP-Seq data." Nucleic acids research 42.D1 (2014): D92-D97 Pubmed PMID: 24297251.
2014
97
BlastR
http://www.tcoffee.org/Projects/blastr/
Finds homologous ncRNAs for the submitted ncRNA sequence.
Bussotti, Giovanni, et al. "BlastR fast and accurate database searches for non-coding RNAs." Nucleic acids research 39.16 (2011): 6886-6895 Pubmed PMID: 21624887 Pubmed Central PMCID: PMC3167602.
2011
98
GATExplorer - Genomic And Transcriptomic Explorer
http://bioinfow.dep.usal.es/xgate/principal.php
Analyzes transcriptomic and expression data, available from microarray in genomic context.
Risueño, Alberto, et al. "GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs." BMC bioinformatics 11.1 (2010): 221 Pubmed PMID: 20429936 Pubmed Central PMCID: PMC2875241.
2010
98
Human Body Map LncRNAs
http://www.broadinstitute.org/genome_bio/human_lincrnas
Catalogs information on 8,000 lincRNAs and these sets of lincRNAs are downloadable.
-
Not available
98
lncRNome
http://genome.igib.res.in/lncRNome/
Comprehensive resource for human lncRNA annotation and their disease associations. It provides an interface to browse across lncRNA datasets.
Bhartiya et al (2012) lncRNome : A comprehensive biologically oriented knowledgebase of long noncoding RNAs Pubmed PMID: 23846593 Pubmed Central PMCID: PMC3708617
2012
99
ncFANs v2 - non-coding RNA Function ANnotation Server
http://www.noncode.org/ncFANs
Web server for functional annotation and functional enrichment of lncRNA.
Liao, Qi, et al. "ncFANs: a web server for functional annotation of long non-coding RNAs." Nucleic acids research 39.suppl 2 (2011): W118-W124 Pubmed PMID: 21715382 Pubmed Central PMCID: PMC3125796.
2011
99
DevMouse
http://www.devmouse.org/
Provides information about methylation patterns of genes , miRNA, lncRNA, and CpG islands in mouse.
Liu, Hongbo, et al. "DevMouse, the mouse developmental methylome database and analysis tools." Database: the journal of biological databases and curation 2014 (2014) Pubmed PMID: 24408217 Pubmed Central PMCID: PMC3885893.
2014
100
linc2GO
http://www.bioinfo.tsinghua.edu.cn/~liuke/Linc2GO/index.html
Provides functional annotations of human lincRNA (GO biological process terms, GO molecular function terms and KEGG pathways). It also links to the Human LincRNA catalog.
Liu, Ke, et al. "Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis." Bioinformatics 29.17 (2013): 2221-2222 Pubmed PMID: 23793747.
2013
100
lncRNABase
http://starbase.sysu.edu.cn/mirLncRNA.php
This database is integrated under starBase. It provides information about the lncRNA and mRNA interactions; information about the ncRNA, RNA-binding protein interactions in pancreatic cancer and compared with normal.
Li, Jun-Hao, et al. "starBase v2. 0: decoding miRNA-ceRNA, miRNA-ncRNA and protein RNA interaction networks from large-scale CLIP-Seq data." Nucleic acids research 42.D1 (2014): D92-D97 Pubmed PMID: 24297251.
2014
100
lncRNAMap (flncRNAdb) - Functional long Non-coding RNA database
http://lncrnamap.mbc.nctu.edu.tw/php/index.php
Gives information about functions of lncRNAs, miRNA regulators of lncRNAs and also interactions between lncRNAs & esiRNAs and their gene targets in human genome.
Chan, Wen-Ling, Hsien-Da Huang, and Jan-Gowth Chang. "lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome." Computational Biology and Chemistry (2014) Pubmed PMID: 24525374.
2014
100
Noncoder v2
http://noncoder.mpi-bn.mpg.de.
Web interface, which provides information about the expression profile of lncRNA using microarray data analysis.
Gellert, Pascal, Yuliya Ponomareva, Thomas Braun, and Shizuka Uchida. "Noncoder: a web interface for exon array-based detection of long non-coding RNAs." Nucleic acids research 41, no. 1 (2013): e20-e20 Pubmed PMID: 23012263 Pubmed Central PMCID: PMC3592461.
2012
100
PlncDB - Plant long non-coding RNA database
http://chualab.rockefeller.edu/gbrowse2/homepage.html
It is a comprehensive resource for Arabidopsis lncRNAs.
Jin, Jingjing, et al. "PLncDB: plant long non-coding RNA database." Bioinformatics 29.8 (2013): 1068-1071 Pubmed PMID: 23476021 Pubmed Central PMCID: PMC3624813.
2013
100
TF2LncRNA
mlg.hit.edu.cn/tf2lncrna
Provides information on transcription factors, which regulate lncRNAs.
Jiang, Qinghua, Jixuan Wang, Yadong Wang, Rui Ma, Xiaoliang Wu, Yu Li, and Yadong Wang. "TF2LncRNA: Identifying common transcription factors for a list of lncRNA genes from ChIP-Seq data."
Not available
100
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