title: Comprehensive prediction of lncRNA-RNA interactions in human transcriptome.
abstract: BACKGROUND
  Recent studies have revealed that large numbers of non-coding RNAs are transcribed in humans, but only a few of them have been identified with their functions. Identification of the interaction target RNAs of the non-coding RNAs is an important step in predicting their functions. The current experimental methods to identify RNA-RNA interactions, however, are not fast enough to apply to a whole human transcriptome. Therefore, computational predictions of RNA-RNA interactions are desirable, but this is a challenging task due to the huge computational costs involved.
  
  
  RESULTS
  Here, we report comprehensive predictions of the interaction targets of lncRNAs in a whole human transcriptome for the first time. To achieve this, we developed an integrated pipeline for predicting RNA-RNA interactions on the K computer, which is one of the fastest super-computers in the world. Comparisons with experimentally-validated lncRNA-RNA interactions support the quality of the predictions. Additionally, we have developed a database that catalogs the predicted lncRNA-RNA interactions to provide fundamental information about the targets of lncRNAs.
authors.affiliation: INTEC Inc, 1-3-3 Shinsuna Koto-ku, Tokyo, 136-8637, Japan.
authors.forename: Goro
authors.initials: G
authors.lastname: Terai
authors.affiliation: Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
authors.forename: Junichi
authors.initials: J
authors.lastname: Iwakiri
authors.affiliation: Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo, 135-0064, Japan.
authors.forename: Tomoshi
authors.initials: T
authors.lastname: Kameda
authors.affiliation: Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo, 135-0064, Japan. mhamada@waseda.jp.|Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo, 169-8555, Japan. mhamada@waseda.jp.
authors.forename: Michiaki
authors.initials: M
authors.lastname: Hamada
authors.affiliation: Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan. asai@k.u-tokyo.ac.jp.|Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo, 135-0064, Japan. asai@k.u-tokyo.ac.jp.
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Asai
mesh_terms: D020413:3' Untranslated Regions; D000465:Algorithms; D030541:Databases, Genetic; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000378:metabolism*; D062085:RNA, Long Noncoding / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D059467:Transcriptome; D016159:Tumor Suppressor Protein p53 / Q000235:genetics; D014584:User-Computer Interface
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D016159:Tumor Suppressor Protein p53
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D764-70
references.pmid: 24270787
references.citation: Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2525-30
references.pmid: 19188602
references.citation: Cell. 2012 Jun 8;149(6):1393-406
references.pmid: 22658674
references.citation: Genome Res. 2012 Sep;22(9):1775-89
references.pmid: 22955988
references.citation: Nucleic Acids Res. 2011 Mar;39(4):e23
references.pmid: 21109538
references.citation: Nature. 2014 May 29;509(7502):582-7
references.pmid: 24870543
references.citation: Nature. 2011 Feb 10;470(7333):284-8
references.pmid: 21307942
references.citation: Int J Mol Sci. 2013 Jun 26;14(7):13307-28
references.pmid: 23803660
references.citation: Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):E3487-96
references.pmid: 23980183
references.citation: Bioinformatics. 2011 Jan 15;27(2):211-9
references.pmid: 21088024
references.citation: Nat Biotechnol. 2005 Nov;23(11):1383-90
references.pmid: 16273071
references.citation: Annu Rev Genet. 2002;36:233-78
references.pmid: 12429693
references.citation: Bioinformatics. 2008 Dec 15;24(24):2849-56
references.pmid: 18940824
references.citation: Brief Funct Genomics. 2015 Jan;14(1):74-89
references.pmid: 25504152
references.citation: Nucleic Acids Res. 2014 Jul;42(Web Server issue):W119-23
references.pmid: 24838564
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D983-6
references.pmid: 23175614
references.citation: Genome Res. 2012 Sep;22(9):1760-74
references.pmid: 22955987
references.citation: EMBO Rep. 2014 May;15(5):489-507
references.pmid: 24731943
references.citation: Bioinformatics. 2010 Sep 15;26(18):i460-6
references.pmid: 20823308
references.citation: J Comput Biol. 2012 May;19(5):532-49
references.pmid: 22313125
references.citation: Nat Rev Genet. 2014 Jun;15(6):423-37
references.pmid: 24776770
references.citation: J Exp Zool B Mol Dev Evol. 2007 Jan 15;308(1):1-25
references.pmid: 17171697
references.citation: RNA Biol. 2012 Jul;9(7):954-65
references.pmid: 22767260
references.citation: Nucleic Acids Res. 2014 Sep;42(15):10099-111
references.pmid: 25123665
references.citation: Nat Biotechnol. 2014 Sep;32(9):933-40
references.pmid: 24997788
references.citation: Cell. 2014 Sep 25;159(1):188-99
references.pmid: 25259926
references.citation: RNA Biol. 2013 Mar;10(3):456-61
references.pmid: 23324609
references.citation: Bioinformatics. 2011 Jul 1;27(13):1788-97
references.pmid: 21531769
references.citation: BMC Bioinformatics. 2010 Feb 09;11:80
references.pmid: 20144198
references.citation: Nature. 2013 Jan 10;493(7431):231-5
references.pmid: 23201690
references.citation: Genome Res. 2011 Mar;21(3):487-93
references.pmid: 21209072
references.citation: Nat Immunol. 2014 Jun;15(6):484-91
references.pmid: 24840979