lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

被引:398
作者
Quek, Xiu Cheng [1 ,2 ]
Thomson, Daniel W. [1 ]
Maag, Jesper L. V. [1 ,2 ]
Bartonicek, Nenad [1 ]
Signal, Bethany [1 ]
Clark, Michael B. [1 ,3 ]
Gloss, Brian S. [1 ,2 ]
Dinger, Marcel E. [1 ,2 ]
机构
[1] Garvan Inst Med Res, Sydney, NSW 2010, Australia
[2] Univ New S Wales, St Vincents Clin Sch, Sydney, NSW 2052, Australia
[3] Univ Oxford, Dept Physiol Anat & Genet, MRC, Funct Genom Unit, Oxford OX1 3PT, England
基金
澳大利亚国家健康与医学研究理事会;
关键词
INTEGRATIVE ANNOTATION; EXPRESSION; TRANSCRIPTION; EVOLUTION; SELECTION; REVEALS; GENCODE; GENOME; CERNA; GENE;
D O I
10.1093/nar/gku988
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. In addition to capturing a great proportion of the recent literature describing functions for individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater accessibility to sequence information, expression data and the literature. The new features in lncRNAdb include the integration of Illumina Body Atlas expression profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct download or a REST API. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration.
引用
收藏
页码:D168 / D173
页数:6
相关论文
共 42 条
  • [1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    Altschul, SF
    Madden, TL
    Schaffer, AA
    Zhang, JH
    Zhang, Z
    Miller, W
    Lipman, DJ
    [J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (17) : 3389 - 3402
  • [2] The eukaryotic genome as an RNA machine
    Amaral, Paulo P.
    Dinger, Marcel E.
    Mercer, Tim R.
    Mattick, John S.
    [J]. SCIENCE, 2008, 319 (5871) : 1787 - 1789
  • [3] lncRNAdb: a reference database for long noncoding RNAs
    Amaral, Paulo P.
    Clark, Michael B.
    Gascoigne, Dennis K.
    Dinger, Marcel E.
    Mattick, John S.
    [J]. NUCLEIC ACIDS RESEARCH, 2011, 39 : D146 - D151
  • [4] SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer
    Askarian-Amiri, Marjan E.
    Crawford, Joanna
    French, Juliet D.
    Smart, Chanel E.
    Smith, Martin A.
    Clark, Michael B.
    Ru, Kelin
    Mercer, Tim R.
    Thompson, Ella R.
    Lakhani, Sunil R.
    Vargas, Ana C.
    Campbell, Ian G.
    Brown, Melissa A.
    Dinger, Marcel E.
    Mattick, John S.
    [J]. RNA, 2011, 17 (05) : 878 - 891
  • [5] Long noncoding RNAs are rarely translated in two human cell lines
    Banfai, Balazs
    Jia, Hui
    Khatun, Jainab
    Wood, Emily
    Risk, Brian
    Gundling, William E., Jr.
    Kundaje, Anshul
    Gunawardena, Harsha P.
    Yu, Yanbao
    Xie, Ling
    Krajewski, Krzysztof
    Strahl, Brian D.
    Chen, Xian
    Bickel, Peter
    Giddings, Morgan C.
    Brown, James B.
    Lipovich, Leonard
    [J]. GENOME RESEARCH, 2012, 22 (09) : 1646 - 1657
  • [6] RNAcentral: A vision for an international database of RNA sequences
    Bateman, Alex
    Agrawal, Shipra
    Birney, Ewan
    Bruford, Elspeth A.
    Bujnicki, Janusz M.
    Cochrane, Guy
    Cole, James R.
    Dinger, Marcel E.
    Enright, Anton J.
    Gardner, Paul P.
    Gautheret, Daniel
    Griffiths-Jones, Sam
    Harrow, Jen
    Herrero, Javier
    Holmes, Ian H.
    Huang, Hsien-Da
    Kelly, Krystyna A.
    Kersey, Paul
    Kozomara, Ana
    Lowe, Todd M.
    Marz, Manja
    Moxon, Simon
    Pruitt, Kim D.
    Samuelsson, Tore
    Stadler, Peter F.
    Vilella, Albert J.
    Vogel, Jan-Hinnerk
    Williams, Kelly P.
    Wright, Mathew W.
    Zwieb, Christian
    [J]. RNA, 2011, 17 (11) : 1941 - 1946
  • [7] Paraspeckles: nuclear bodies built on long noncoding RNA
    Bond, Charles S.
    Fox, Archa H.
    [J]. JOURNAL OF CELL BIOLOGY, 2009, 186 (05) : 637 - 644
  • [8] NONCODE v3.0: integrative annotation of long noncoding RNAs
    Bu, Dechao
    Yu, Kuntao
    Sun, Silong
    Xie, Chaoyong
    Skogerbo, Geir
    Miao, Ruoyu
    Xiao, Hui
    Liao, Qi
    Luo, Haitao
    Zhao, Guoguang
    Zhao, Haitao
    Liu, Zhiyong
    Liu, Changning
    Chen, Runsheng
    Zhao, Yi
    [J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) : D210 - D215
  • [9] Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    Cabili, Moran N.
    Trapnell, Cole
    Goff, Loyal
    Koziol, Magdalena
    Tazon-Vega, Barbara
    Regev, Aviv
    Rinn, John L.
    [J]. GENES & DEVELOPMENT, 2011, 25 (18) : 1915 - 1927
  • [10] InCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA
    Das, Shaoli
    Ghosal, Suman
    Sen, Rituparno
    Chakrabarti, Jayprokas
    [J]. PLOS ONE, 2014, 9 (06):