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Volumn 4, Issue 4, 2012, Pages 427-442

Identification and properties of 1,119 candidate LincRNA loci in the Drosophila melanogaster genome

Author keywords

Development; Evolution; Long intergenic noncoding RNAs; ModENCODE; Transcriptional regulation

Indexed keywords

DROSOPHILA MELANOGASTER; INVERTEBRATA; MAMMALIA; VERTEBRATA;

EID: 84864098110     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs020     Document Type: Conference Paper
Times cited : (172)

References (75)
  • 2
    • 27144491328 scopus 로고    scopus 로고
    • Adaptive evolution of non-coding DNA in Drosophila
    • DOI 10.1038/nature04107, PII N04107
    • Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437(7062):1149-1152. (Pubitemid 41509351)
    • (2005) Nature , vol.437 , Issue.7062 , pp. 1149-1152
    • Andolfatto, P.1
  • 3
    • 68749096120 scopus 로고    scopus 로고
    • Ontogeny and phylogeny: Molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila
    • Artieri CG, Haerty W, Singh RS. 2009. Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila. BMC Biol. 7:42.
    • (2009) BMC Biol. , vol.7 , pp. 42
    • Artieri, C.G.1    Haerty, W.2    Singh, R.S.3
  • 5
    • 38549122308 scopus 로고    scopus 로고
    • InParanoid 6: Eukaryotic ortholog clusters with inparalogs
    • DOI 10.1093/nar/gkm1020
    • Berglund AC, Sjolund E, Ostlund G, Sonnhammer ELL. 2007. InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 36: (Database):D263-D266 (Pubitemid 351149733)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Berglund, A.-C.1    Sjolund, E.2    Ostlund, G.3    Sonnhammer, E.L.L.4
  • 6
    • 77956882723 scopus 로고    scopus 로고
    • A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression
    • Bernard D, et al. 2010. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J. 29(18):3082-3093.
    • (2010) EMBO J. , vol.29 , Issue.18 , pp. 3082-3093
    • Bernard, D.1
  • 8
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN, et al. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25(18):1915-1927.
    • (2011) Genes Dev. , vol.25 , Issue.18 , pp. 1915-1927
    • Cabili, M.N.1
  • 9
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • Carninci P, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309(5740):1559-1563.
    • (2005) Science , vol.309 , Issue.5740 , pp. 1559-1563
    • Carninci, P.1
  • 10
    • 77954399763 scopus 로고    scopus 로고
    • Long noncoding RNA genes: Conservation of sequence and brain expression among diverse amniotes
    • Chodroff RA, et al. 2010. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol. 11(7):R72.
    • (2010) Genome Biol. , vol.11 , Issue.7
    • Chodroff, R.A.1
  • 11
    • 79960911703 scopus 로고    scopus 로고
    • The reality of pervasive transcription
    • discussion e1001102
    • Clark MB, et al. 2011. The reality of pervasive transcription. PLoS Biol. 9(7):e1000625. discussion e1001102.
    • (2011) PLoS Biol. , vol.9 , Issue.7
    • Clark, M.B.1
  • 14
    • 21244484614 scopus 로고    scopus 로고
    • Protein evolution in the context of Drosophila development
    • DOI 10.1007/s00239-004-0241-2
    • Davis JC, Brandman O, Petrov DA. 2005. Protein evolution in the context of Drosophila development. J Mol Evol. 60(6):774-785. (Pubitemid 40896554)
    • (2005) Journal of Molecular Evolution , vol.60 , Issue.6 , pp. 774-785
    • Davis, J.C.1    Brandman, O.2    Petrov, D.A.3
  • 15
    • 33747798962 scopus 로고    scopus 로고
    • Non-coding RNA in fly dosage compensation
    • DOI 10.1016/j.tibs.2006.07.007, PII S0968000406001988
    • Deng X, Meller VH. 2006. Non-coding RNA in fly dosage compensation. Trends Biochem Sci. 31(9):526-532. (Pubitemid 44279985)
    • (2006) Trends in Biochemical Sciences , vol.31 , Issue.9 , pp. 526-532
    • Deng, X.1    Meller, V.H.2
  • 16
    • 43049127826 scopus 로고    scopus 로고
    • PeptideAtlas: A resource for target selection for emerging targeted proteomics workflows
    • DOI 10.1038/embor.2008.56, PII EMBOR200856
    • Deutsch EW, Lam H, Aebersold R. 2008. PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9(5):429-434. (Pubitemid 351627279)
    • (2008) EMBO Reports , vol.9 , Issue.5 , pp. 429-434
    • Deutsch, E.W.1    Lam, H.2    Aebersold, R.3
  • 17
    • 0033977618 scopus 로고    scopus 로고
    • Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
    • Duret L, Mouchiroud D. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol. 17(1):68-74. (Pubitemid 30056993)
    • (2000) Molecular Biology and Evolution , vol.17 , Issue.1 , pp. 68-74
    • Duret, L.1    Mouchiroud, D.2
  • 18
    • 33646473694 scopus 로고    scopus 로고
    • Complex loci in human and mouse genomes
    • Engström PG, et al. 2006. Complex loci in human and mouse genomes. PLoS Genet. 2(4):e47.
    • (2006) PLoS Genet. , vol.2 , Issue.4
    • Engström, P.G.1
  • 19
    • 77957776228 scopus 로고    scopus 로고
    • Systematic protein location mapping reveals five principal chromatin types in Drosophila cells
    • Filion GJ, et al. 2010. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143(2): 212-224.
    • (2010) Cell , vol.143 , Issue.2 , pp. 212-224
    • Filion, G.J.1
  • 20
    • 79953043801 scopus 로고    scopus 로고
    • The developmental transcriptome of Drosophila melanogaster
    • Graveley BR, et al. 2011. The developmental transcriptome of Drosophila melanogaster. Nature 471(7339):473-479.
    • (2011) Nature , vol.471 , Issue.7339 , pp. 473-479
    • Graveley, B.R.1
  • 21
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • Guttman M, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235):223-227.
    • (2009) Nature , vol.458 , Issue.7235 , pp. 223-227
    • Guttman, M.1
  • 22
    • 80052869283 scopus 로고    scopus 로고
    • LincRNAs act in the circuitry controlling pluripotency and differentiation
    • Guttman M, et al. 2011. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477(7364):295-300.
    • (2011) Nature , vol.477 , Issue.7364 , pp. 295-300
    • Guttman, M.1
  • 23
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman M, et al. 2010. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol. 28(5):503-510.
    • (2010) Nat Biotechnol. , vol.28 , Issue.5 , pp. 503-510
    • Guttman, M.1
  • 24
    • 25844481290 scopus 로고    scopus 로고
    • Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content
    • Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P. 2005. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol. 6(8):R67.
    • (2005) Genome Biol. , vol.6 , Issue.8
    • Haddrill, P.R.1    Charlesworth, B.2    Halligan, D.L.3    Andolfatto, P.4
  • 26
    • 67650022866 scopus 로고    scopus 로고
    • Conserved introns reveal novel transcripts in Drosophila melanogaster
    • Hiller M, et al. 2009. Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Res. 19(7):1289-1300.
    • (2009) Genome Res. , vol.19 , Issue.7 , pp. 1289-1300
    • Hiller, M.1
  • 27
    • 17644396621 scopus 로고    scopus 로고
    • Non-coding RNAs: Hope or hype?
    • DOI 10.1016/j.tig.2005.03.007
    • Hüttenhofer A, Schattner P, Polacek N. 2005. Non-coding RNAs: hope or hype? Trends Genet. 21(5):289-297. (Pubitemid 40558935)
    • (2005) Trends in Genetics , vol.21 , Issue.5 , pp. 289-297
    • Huttenhofer, A.1    Schattner, P.2    Polacek, N.3
  • 28
    • 29244485152 scopus 로고    scopus 로고
    • Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila
    • DOI 10.1111/j.1365-2443.2005.00910.x
    • Inagaki S, et al. 2005. Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila. Genes Cells. 10(12):1163-1173. (Pubitemid 41830075)
    • (2005) Genes to Cells , vol.10 , Issue.12 , pp. 1163-1173
    • Inagaki, S.1    Numata, K.2    Kondo, T.3    Tomita, M.4    Yasuda, K.5    Kanai, A.6    Kageyama, Y.7
  • 29
    • 12344291073 scopus 로고    scopus 로고
    • Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments
    • DOI 10.1016/j.tig.2004.12.009, PII S0168952504003373
    • Johnson JM, Edwards S, Shoemaker D, Schadt EE. 2005. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21(2):93-102. (Pubitemid 40127353)
    • (2005) Trends in Genetics , vol.21 , Issue.2 , pp. 93-102
    • Johnson, J.M.1    Edwards, S.2    Shoemaker, D.3    Schadt, E.E.4
  • 30
    • 33751018566 scopus 로고    scopus 로고
    • Human sat III and Drosophila hsr omega transcripts: A common paradigm for regulation of nuclear RNA processing in stressed cells
    • DOI 10.1093/nar/gkl711
    • Jolly C, Lakhotia SC. 2006. Human sat III and Drosophila hsr omega transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells. Nucleic Acids Res. 34(19):5508-5514. (Pubitemid 44742439)
    • (2006) Nucleic Acids Research , vol.34 , Issue.19 , pp. 5508-5514
    • Jolly, C.1    Lakhotia, S.C.2
  • 31
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • DOI 10.1101/gr.229202. Article published online before March 2002
    • Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12(4):656-664. (Pubitemid 34308645)
    • (2002) Genome Research , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 32
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent WJ, et al. 2002. The human genome browser at UCSC. Genome Res. 12(6):996-1006.
    • (2002) Genome Res. , vol.12 , Issue.6 , pp. 996-1006
    • Kent, W.J.1
  • 33
    • 34547582418 scopus 로고    scopus 로고
    • CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine
    • (Web Server issue)
    • Kong L, et al. 2007. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 35 (Web Server issue): W345-W349.
    • (2007) Nucleic Acids Res. , vol.35
    • Kong, L.1
  • 34
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10(3):R25.
    • (2009) Genome Biol. , vol.10 , Issue.3
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 35
    • 67949086754 scopus 로고    scopus 로고
    • Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster
    • Li Z, et al. 2009. Detection of intergenic non-coding RNAs expressed in the main developmental stages in Drosophila melanogaster. Nucleic Acids Res. 37(13):4308-4314.
    • (2009) Nucleic Acids Res. , vol.37 , Issue.13 , pp. 4308-4314
    • Li, Z.1
  • 36
    • 79959446962 scopus 로고    scopus 로고
    • PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions
    • Lin MF, Jungreis I, Kellis M. 2011. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics 27(13):i275-i282.
    • (2011) Bioinformatics , vol.27 , Issue.13
    • Lin, M.F.1    Jungreis, I.2    Kellis, M.3
  • 37
    • 0023332565 scopus 로고
    • Novel transcripts from the ultrabithorax domain of the bithorax complex
    • Lipshitz HD, Peattie DA, Hogness DS. 1987. Novel transcripts from the ultrabithorax domain of the bithorax complex. Genes Dev. 1(3): 307-322.
    • (1987) Genes Dev. , vol.1 , Issue.3 , pp. 307-322
    • Lipshitz, H.D.1    Peattie, D.A.2    Hogness, D.S.3
  • 38
    • 39049145326 scopus 로고    scopus 로고
    • Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
    • DOI 10.1101/gr.6725608
    • Lunter G, et al. 2008. Uncertainty in homology inferences: assessing and improving genomic sequence alignment. Genome Res. 18(2): 298-309. (Pubitemid 351240740)
    • (2008) Genome Research , vol.18 , Issue.2 , pp. 298-309
    • Lunter, G.1    Rocco, A.2    Mimouni, N.3    Heger, A.4    Caldeira, A.5    Hein, J.6
  • 39
    • 76249108851 scopus 로고    scopus 로고
    • Catalogues of mammalian long noncoding RNAs: Modest conservation and incompleteness
    • Marques AC, Ponting CP. 2009. Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol. 10(11):R124.
    • (2009) Genome Biol. , vol.10 , Issue.11
    • Marques, A.C.1    Ponting, C.P.2
  • 40
    • 0141867857 scopus 로고    scopus 로고
    • Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms
    • DOI 10.1002/bies.10332
    • Mattick JS. 2003. Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. BioEssays 25(10): 930-939. (Pubitemid 37221517)
    • (2003) BioEssays , vol.25 , Issue.10 , pp. 930-939
    • Mattick, J.S.1
  • 41
    • 0026428610 scopus 로고
    • Adaptive protein evolution at the Adh locus in Drosophila
    • McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351(6328):652-654. (Pubitemid 21896661)
    • (1991) Nature , vol.351 , Issue.6328 , pp. 652-654
    • McDonald, J.H.1    Kreitman, M.2
  • 42
    • 78149408021 scopus 로고    scopus 로고
    • Massive turnover of functional sequence in human and other mammalian genomes
    • Meader S, Ponting CP, Lunter G. 2010. Massive turnover of functional sequence in human and other mammalian genomes. Genome Res. 20(10):1335-1343.
    • (2010) Genome Res. , vol.20 , Issue.10 , pp. 1335-1343
    • Meader, S.1    Ponting, C.P.2    Lunter, G.3
  • 44
    • 77149173174 scopus 로고    scopus 로고
    • Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and microRNA biogenesis pathways in Drosophila
    • Miyoshi K, Miyoshi T, Hartig JV, Siomi H, Siomi MC. 2010. Molecular mechanisms that funnel RNA precursors into endogenous small-interfering RNA and microRNA biogenesis pathways in Drosophila. RNA 16:506-515.
    • (2010) RNA , vol.16 , pp. 506-515
    • Miyoshi, K.1    Miyoshi, T.2    Hartig, J.V.3    Siomi, H.4    Siomi, M.C.5
  • 45
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • DOI 10.1038/nmeth.1226, PII NMETH.1226
    • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 5(7):621-628. (Pubitemid 351911867)
    • (2008) Nature Methods , vol.5 , Issue.7 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 46
    • 77957243921 scopus 로고    scopus 로고
    • Long noncoding RNAs with enhancer-like function in human cells
    • Ørom UA, et al. 2010. Long noncoding RNAs with enhancer-like function in human cells. Cell 143(1):46-58.
    • (2010) Cell , vol.143 , Issue.1 , pp. 46-58
    • Ørom, U.A.1
  • 47
    • 2242492681 scopus 로고    scopus 로고
    • Extent of chromatin spreading determined by roX RNA recruitment of MSL proteins
    • DOI 10.1126/science.1076686
    • Park Y, Kelley RL, Oh H, Kuroda MI, Meller VH. 2002. Extent of chromatin spreading determined by roX RNA recruitment of MSL proteins. Science 298(5598):1620-1623. (Pubitemid 35387200)
    • (2002) Science , vol.298 , Issue.5598 , pp. 1620-1623
    • Park, Y.1    Kelley, R.L.2    Oh, H.3    Kuroda, M.I.4    Meller, V.H.5
  • 48
    • 70149123708 scopus 로고    scopus 로고
    • Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
    • Ponjavic J, Oliver PL, Lunter G, Ponting CP. 2009. Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet. 5(8): e1000617.
    • (2009) PLoS Genet. , vol.5 , Issue.8
    • Ponjavic, J.1    Oliver, P.L.2    Lunter, G.3    Ponting, C.P.4
  • 49
    • 34248162440 scopus 로고    scopus 로고
    • Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
    • DOI 10.1101/gr.6036807
    • Ponjavic J, Ponting CP, Lunter G. 2007. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res. 17(5):556-565. (Pubitemid 46715505)
    • (2007) Genome Research , vol.17 , Issue.5 , pp. 556-565
    • Ponjavic, J.1    Ponting, C.P.2    Lunter, G.3
  • 50
    • 49949090861 scopus 로고    scopus 로고
    • The functional repertoires of metazoan genomes
    • Ponting CP. 2008. The functional repertoires of metazoan genomes. Nat Rev Genet. 9(9):689.
    • (2008) Nat Rev Genet. , vol.9 , Issue.9 , pp. 689
    • Ponting, C.P.1
  • 51
    • 78651481549 scopus 로고    scopus 로고
    • Transcribed dark matter: Meaning or myth?
    • Ponting CP, Belgard TG. 2010. Transcribed dark matter: meaning or myth? Hum Mol Genet. 19(R2):R162-R168.
    • (2010) Hum Mol Genet , vol.19 , Issue.R2
    • Ponting, C.P.1    Belgard, T.G.2
  • 52
    • 60149099385 scopus 로고    scopus 로고
    • Evolution and functions of long noncoding RNAs
    • Ponting CP, Oliver PL, Reik W. 2009. Evolution and functions of long noncoding RNAs. Cell 136(4):629-641.
    • (2009) Cell , vol.136 , Issue.4 , pp. 629-641
    • Ponting, C.P.1    Oliver, P.L.2    Reik, W.3
  • 53
    • 33846169089 scopus 로고    scopus 로고
    • Eukaryotic regulatory RNAs: An answer to the 'genome complexity' conundrum
    • DOI 10.1101/gad.1484207
    • Prasanth KV, Spector DL. 2007. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev. 21(1):11-42. (Pubitemid 46089704)
    • (2007) Genes and Development , vol.21 , Issue.1 , pp. 11-42
    • Prasanth, K.V.1    Spector, D.L.2
  • 55
    • 77954631472 scopus 로고    scopus 로고
    • Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster
    • Rogers RL, Bedford T, Lyons AM, Hartl DL. 2010. Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster. Proc Natl Acad Sci U S A. 107(24):10943-10948.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , Issue.24 , pp. 10943-10948
    • Rogers, R.L.1    Bedford, T.2    Lyons, A.M.3    Hartl, D.L.4
  • 56
    • 38149071979 scopus 로고    scopus 로고
    • Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    • DOI 10.1101/gr.6597907
    • Ruby JG, et al. 2007. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila micro-RNAs. Genome Res. 17(12):1850-1864. (Pubitemid 351360008)
    • (2007) Genome Research , vol.17 , Issue.12 , pp. 1850-1864
    • Ruby, J.G.1    Stark, A.2    Johnston, W.K.3    Kellis, M.4    Bartel, D.P.5    Lai, E.C.6
  • 57
    • 33644514069 scopus 로고    scopus 로고
    • Noncoding RNAs of trithorax response elements recruit Drosophila ash1 to Ultrabithorax
    • Sanchez-Elsner T, Gou D, Kremmer E, Sauer F. 2006. Noncoding RNAs of trithorax response elements recruit Drosophila ash1 to Ultrabithorax. Science 311(5764):1118-1123.
    • (2006) Science , vol.311 , Issue.5764 , pp. 1118-1123
    • Sanchez-Elsner, T.1    Gou, D.2    Kremmer, E.3    Sauer, F.4
  • 60
    • 33750379420 scopus 로고    scopus 로고
    • Polycomb silencers control cell fate, development and cancer
    • DOI 10.1038/nrc1991, PII NRC1991
    • Sparmann A, van Lohuizen M. 2006. Polycomb silencers control cell fate, development, and cancer. Nat Rev Cancer 6:846-856. (Pubitemid 44629896)
    • (2006) Nature Reviews Cancer , vol.6 , Issue.11 , pp. 846-856
    • Sparmann, A.1    Van Lohuizen, M.2
  • 61
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105-1111.
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 62
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, et al. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 28(5):511-515.
    • (2010) Nat Biotechnol. , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1
  • 63
    • 77956927823 scopus 로고    scopus 로고
    • The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation
    • Tripathi V, et al. 2010. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell. 39(6):925-938.
    • (2010) Mol Cell. , vol.39 , Issue.6 , pp. 925-938
    • Tripathi, V.1
  • 65
    • 58149199579 scopus 로고    scopus 로고
    • FlyBase: Enhancing Drosophila Gene Ontology annotations
    • (Database issue)
    • Tweedie S, et al. 2009. FlyBase: enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res. 37: (Database issue):D555-D559.
    • (2009) Nucleic Acids Res. , vol.37
    • Tweedie, S.1
  • 66
    • 77952905505 scopus 로고    scopus 로고
    • Most "dark matter" transcripts are associated with known genes
    • van Bakel H, Nislow C, Blencowe BJ, Hughes TR. 2010. Most "dark matter" transcripts are associated with known genes. PLoS Biol. 8(5):e1000371.
    • (2010) PLoS Biol. , vol.8 , Issue.5
    • Van Bakel, H.1    Nislow, C.2    Blencowe, B.J.3    Hughes, T.R.4
  • 67
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 10(1):57-63.
    • (2009) Nat Rev Genet. , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 69
    • 67649671961 scopus 로고    scopus 로고
    • Long noncoding RNAs: Functional surprises from the RNA world
    • Wilusz JE, Sunwoo H, Spector DL. 2009. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 23(13): 1494-1504.
    • (2009) Genes Dev. , vol.23 , Issue.13 , pp. 1494-1504
    • Wilusz, J.E.1    Sunwoo, H.2    Spector, D.L.3
  • 70
    • 0347766006 scopus 로고    scopus 로고
    • Elevated rates of protein secretion, evolution, and disease among tissue-specific genes
    • DOI 10.1101/gr.1924004
    • Winter EE, Goodstadt L, Ponting CP. 2004. Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Res. 14(1):54-61. (Pubitemid 38088525)
    • (2004) Genome Research , vol.14 , Issue.1 , pp. 54-61
    • Winter, E.E.1    Goodstadt, L.2    Ponting, C.P.3
  • 71
    • 20044366725 scopus 로고    scopus 로고
    • Highly conserved non-coding sequences are associated with vertebrate development
    • Woolfe A, et al. 2004. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3(1):e7.
    • (2004) PLoS Biol. , vol.3 , Issue.1
    • Woolfe, A.1
  • 72
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • DOI 10.1093/molbev/msm088
    • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24(8):1586-1591. (Pubitemid 47236688)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.1
  • 73
    • 34948831152 scopus 로고    scopus 로고
    • Noncoding but nonexpendable: Transcriptional regulation by large noncoding RNA in eukaryotes
    • DOI 10.1139/O07-061
    • Yazgan O, Krebs JE. 2007. Noncoding but nonexpendable: transcriptional regulation by large noncoding RNA in eukaryotes. Biochem Cell Biol. 85(4):484-496. (Pubitemid 47518043)
    • (2007) Biochemistry and Cell Biology , vol.85 , Issue.4 , pp. 484-496
    • Yazgan, O.1    Krebs, J.E.2
  • 74
    • 36048937264 scopus 로고    scopus 로고
    • An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster
    • DOI 10.1038/nature06263, PII NATURE06263
    • Yin H, Lin H. 2007. An epigenetic activation role of Piwi and a Piwi-associated piRNA in Drosophila melanogaster. Nature 450(7167):304-308. (Pubitemid 350100538)
    • (2007) Nature , vol.450 , Issue.7167 , pp. 304-308
    • Yin, H.1    Lin, H.2
  • 75
    • 78650253763 scopus 로고    scopus 로고
    • Genome-wide identification of polycomb-associated RNAs by RIP-seq
    • Zhao J, et al. 2010. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell. 40(6):939-953.
    • (2010) Mol Cell. , vol.40 , Issue.6 , pp. 939-953
    • Zhao, J.1


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