| 1 |
Rfamhttp://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 |
|
| 2 |
lncRNAdbhttp://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 |
|
| 3 |
FRNAdb 3.0 - Functional RNA databasehttp://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 |
|
| 4 |
NONCODEv4 / NONCODEv3http://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 |
|
| 5 |
NRED- nc rna expression databasehttp://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 |
|
| 6 |
LNCipediahttp://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 |
|
| 7 |
LncRNADisease - The LncRNA and Disease Databasehttp://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 |
|
| 8 |
HGNC - HUGO Gene Nomenclature Committeehttp://www.genenames.org/rna/LNCRNA |
Provides comprehensive annotations of eukaryotic lncRNAs, which is taken from lncRNAdb. | | 2013 | 93 |
|
| 9 |
ChIPBasehttp://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 |
|
| 10 |
ncRNAimprinthttp://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 |
URL not working as on 26 Feb 2014 |
| 11 |
DIANA-LncBasewww.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 |
|
| 12 |
iSeeRNAhttp://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 |
|
| 13 |
NPInterhttp://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 |
|
| 14 |
starBase v2.0http://starbase.sysu.edu.cn/index.php |
Provides information about interactions between ncRNAs and, also ncRNA and protein. | L i , J u n - H a o , e t a l . " s t a r B a s e v 2 . 0 : d e c o d i n g m i R N A - c e R N A , m i R N A - n c R N A a n d p r o t e i n R N A i n t e r a c t i o n n e t w o r k s f r o m l a r g e - s c a l e C L I P - S e q d a t a . " N u c l e i c a c i d s r e s e a r c h 4 2 . D 1 ( 2 0 1 4 ) : D 9 2 - D 9 7 P u b m e d P M I D : 2 4 2 9 7 2 5 1 .
| 2014 | 97 |
|
| 15 |
BlastRhttp://www.tcoffee.org/Projects/blastr/ |
Finds homologous ncRNAs for the submitted ncRNA sequence. | B u s s o t t i , G i o v a n n i , e t a l . " B l a s t R f a s t a n d a c c u r a t e d a t a b a s e s e a r c h e s f o r n o n - c o d i n g R N A s . " N u c l e i c a c i d s r e s e a r c h 3 9 . 1 6 ( 2 0 1 1 ) : 6 8 8 6 - 6 8 9 5 P u b m e d P M I D : 2 1 6 2 4 8 8 7 P u b m e d C e n t r a l P M C I D : P M C 3 1 6 7 6 0 2 .
| 2011 | 98 |
|
| 16 |
GATExplorer - Genomic And Transcriptomic Explorerhttp://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 |
|
| 17 |
Human Body Map LncRNAshttp://www.broadinstitute.org/genome_bio/human_lincrnas |
Catalogs information on 8,000 lincRNAs and these sets of lincRNAs are downloadable. | | Not available | 98 |
|
| 18 |
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 |
|
| 19 |
ncFANs v2 - non-coding RNA Function ANnotation Serverhttp://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 |
|
| 20 |
DevMousehttp://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 |
URL not working as on 26 Feb 2014 |
| 21 |
linc2GOhttp://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 |
|
| 22 |
lncRNABasehttp://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. | L i , J u n - H a o , e t a l . " s t a r B a s e v 2 . 0 : d e c o d i n g m i R N A - c e R N A , m i R N A - n c R N A a n d p r o t e i n R N A i n t e r a c t i o n n e t w o r k s f r o m l a r g e - s c a l e C L I P - S e q d a t a . " N u c l e i c a c i d s r e s e a r c h 4 2 . D 1 ( 2 0 1 4 ) : D 9 2 - D 9 7 P u b m e d P M I D : 2 4 2 9 7 2 5 1 .
| 2014 | 100 |
|
| 23 |
lncRNAMap (flncRNAdb) - Functional long Non-coding RNA databasehttp://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 |
|
| 24 |
Noncoder v2http://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 |
|
| 25 |
PlncDB - Plant long non-coding RNA databasehttp://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 |
|
| 26 |
TF2LncRNAmlg.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 |
|
