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Volumn 47, Issue 3, 2015, Pages 199-208

The landscape of long noncoding RNAs in the human transcriptome

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; TRANSCRIPTOME;

EID: 84924063355     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3192     Document Type: Article
Times cited : (2279)

References (61)
  • 1
    • 84918815964 scopus 로고    scopus 로고
    • Cancer incidence and mortality worldwide: Sources, methods and major patterns in GLOBOCAN 2012
    • Ferlay, J. et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int. J. Cancer 136, E359-E386 (2015).
    • (2015) Int. J. Cancer , vol.136 , pp. E359-E386
    • Ferlay, J.1
  • 2
    • 84885735554 scopus 로고    scopus 로고
    • Mutational landscape and significance across 12 major cancer types
    • Kandoth, C. et al. Mutational landscape and significance across 12 major cancer types. Nature 502, 333-339 (2013).
    • (2013) Nature , vol.502 , pp. 333-339
    • Kandoth, C.1
  • 3
    • 84884997982 scopus 로고    scopus 로고
    • Emerging landscape of oncogenic signatures across human cancers
    • Ciriello, G. et al. Emerging landscape of oncogenic signatures across human cancers. Nat. Genet. 45, 1127-1133 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 1127-1133
    • Ciriello, G.1
  • 4
    • 84865757142 scopus 로고    scopus 로고
    • Landscape of transcription in human cells
    • Djebali, S. et al. Landscape of transcription in human cells. Nature 489, 101-108 (2012).
    • (2012) Nature , vol.489 , pp. 101-108
    • Djebali, S.1
  • 5
    • 84879987789 scopus 로고    scopus 로고
    • lincRNAs: Genomics, evolution, and mechanisms
    • Ulitsky, I. & Bartel, D.P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26-46 (2013).
    • (2013) Cell , vol.154 , pp. 26-46
    • Ulitsky, I.1    Bartel, D.P.2
  • 6
    • 82155186923 scopus 로고    scopus 로고
    • The emergence of lncRNAs in cancer biology
    • Prensner, J.R. & Chinnaiyan, A.M. The emergence of lncRNAs in cancer biology. Cancer Discov. 1, 391-407 (2011).
    • (2011) Cancer Discov. , vol.1 , pp. 391-407
    • Prensner, J.R.1    Chinnaiyan, A.M.2
  • 7
    • 84872198346 scopus 로고    scopus 로고
    • Differential analysis of gene regulation at transcript resolution with RNA-seq
    • Trapnell, C. et al. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31, 46-53 (2013).
    • (2013) Nat. Biotechnol. , vol.31 , pp. 46-53
    • Trapnell, C.1
  • 8
    • 84888871954 scopus 로고    scopus 로고
    • Assessment of transcript reconstruction methods for RNA-seq
    • Steijger, T. et al. Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods 10, 1177-1184 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1177-1184
    • Steijger, T.1
  • 9
    • 79961202865 scopus 로고    scopus 로고
    • Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
    • Prensner, J.R. et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat. Biotechnol. 29, 742-749 (2011).
    • (2011) Nat. Biotechnol. , vol.29 , pp. 742-749
    • Prensner, J.R.1
  • 10
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: The reference human genome annotation for The ENCODE Project
    • Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760-1774 (2012).
    • (2012) Genome Res. , vol.22 , pp. 1760-1774
    • Harrow, J.1
  • 11
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili, M.N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
    • (2011) Genes Dev. , vol.25 , pp. 1915-1927
    • Cabili, M.N.1
  • 12
    • 84891767394 scopus 로고    scopus 로고
    • RefSeq: An update on mammalian reference sequences
    • Pruitt, K.D. et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 42, D756-D763 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D756-D763
    • Pruitt, K.D.1
  • 13
    • 84891771466 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: 2014 update
    • Karolchik, D. et al. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 42, D764-D770 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D764-D770
    • Karolchik, D.1
  • 14
    • 84876020023 scopus 로고    scopus 로고
    • CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model
    • Wang, L. et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 41, e74 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. e74
    • Wang, L.1
  • 15
    • 84891782659 scopus 로고    scopus 로고
    • Pfam: The protein families database
    • Finn, R.D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222-D230 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D222-D230
    • Finn, R.D.1
  • 16
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim, M.S. et al. A draft map of the human proteome. Nature 509, 575-581 (2014).
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.S.1
  • 17
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789 (2012).
    • (2012) Genome Res. , vol.22 , pp. 1775-1789
    • Derrien, T.1
  • 18
    • 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. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 503-510
    • Guttman, M.1
  • 19
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
    • (2012) Nature , vol.489 , pp. 57-74
  • 20
    • 84875945705 scopus 로고    scopus 로고
    • ENCODE data in the UCSC genome browser: Year 5 update
    • Rosenbloom, K.R. et al. ENCODE data in the UCSC genome browser: year 5 update. Nucleic Acids Res. 41, D56-D63 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D56-D63
    • Rosenbloom, K.R.1
  • 21
    • 84895908120 scopus 로고    scopus 로고
    • The evolution of lncRNA repertoires and expression patterns in tetrapods
    • Necsulea, A. et al. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 505, 635-640 (2014).
    • (2014) Nature , vol.505 , pp. 635-640
    • Necsulea, A.1
  • 22
    • 84876541696 scopus 로고    scopus 로고
    • UCNEbase - A database of ultraconserved non-coding elements and genomic regulatory blocks
    • Dimitrieva, S. & Bucher, P. UCNEbase - A database of ultraconserved non-coding elements and genomic regulatory blocks. Nucleic Acids Res. 41, D101-D109 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D101-D109
    • Dimitrieva, S.1    Bucher, P.2
  • 23
    • 2542542256 scopus 로고    scopus 로고
    • Ultraconserved elements in the human genome
    • Bejerano, G. et al. Ultraconserved elements in the human genome. Science 304, 1321-1325 (2004).
    • (2004) Science , vol.304 , pp. 1321-1325
    • Bejerano, G.1
  • 24
    • 84891790401 scopus 로고    scopus 로고
    • The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
    • Welter, D. et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42, D1001-D1006 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D1001-D1006
    • Welter, D.1
  • 25
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550 (2005).
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1
  • 26
    • 84863723010 scopus 로고    scopus 로고
    • The mutational landscape of lethal castration-resistant prostate cancer
    • Grasso, C.S. et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature 487, 239-243 (2012).
    • (2012) Nature , vol.487 , pp. 239-243
    • Grasso, C.S.1
  • 27
    • 4344561557 scopus 로고    scopus 로고
    • Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy
    • Yu, Y.P. et al. Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J. Clin. Oncol. 22, 2790-2799 (2004).
    • (2004) J. Clin. Oncol. , vol.22 , pp. 2790-2799
    • Yu, Y.P.1
  • 28
    • 77954255681 scopus 로고    scopus 로고
    • Integrative genomic profiling of human prostate cancer
    • Taylor, B.S. et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 18, 11-22 (2010).
    • (2010) Cancer Cell , vol.18 , pp. 11-22
    • Taylor, B.S.1
  • 29
    • 84856002018 scopus 로고    scopus 로고
    • TP53 genomics predict higher clinical and pathologic tumor response in operable early-stage breast cancer treated with docetaxel-capecitabine ± trastuzumab
    • Glück, S. et al. TP53 genomics predict higher clinical and pathologic tumor response in operable early-stage breast cancer treated with docetaxel-capecitabine ± trastuzumab. Breast Cancer Res. Treat. 132, 781-791 (2012).
    • (2012) Breast Cancer Res. Treat. , vol.132 , pp. 781-791
    • Glück, S.1
  • 30
    • 84861527388 scopus 로고    scopus 로고
    • The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
    • Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346-352 (2012).
    • (2012) Nature , vol.486 , pp. 346-352
    • Curtis, C.1
  • 31
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).
    • (2012) Nature , vol.490 , pp. 61-70
  • 32
    • 33847246805 scopus 로고    scopus 로고
    • Oncomine 3.0: Genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles
    • Rhodes, D.R. et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9, 166-180 (2007).
    • (2007) Neoplasia , vol.9 , pp. 166-180
    • Rhodes, D.R.1
  • 34
    • 84870261155 scopus 로고    scopus 로고
    • LIFR is a breast cancer metastasis suppressor upstream of the Hippo-YAP pathway and a prognostic marker
    • Chen, D. et al. LIFR is a breast cancer metastasis suppressor upstream of the Hippo-YAP pathway and a prognostic marker. Nat. Med. 18, 1511-1517 (2012).
    • (2012) Nat. Med. , vol.18 , pp. 1511-1517
    • Chen, D.1
  • 35
    • 77951118936 scopus 로고    scopus 로고
    • Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis
    • Gupta, R.A. et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076 (2010).
    • (2010) Nature , vol.464 , pp. 1071-1076
    • Gupta, R.A.1
  • 36
    • 84887122461 scopus 로고    scopus 로고
    • The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex
    • Prensner, J.R. et al. The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat. Genet. 45, 1392-1398 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 1392-1398
    • Prensner, J.R.1
  • 37
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227 (2009).
    • (2009) Nature , vol.458 , pp. 223-227
    • Guttman, M.1
  • 38
    • 67349158067 scopus 로고    scopus 로고
    • A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1)
    • Thomas, G. et al. A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nat. Genet. 41, 579-584 (2009).
    • (2009) Nat. Genet. , vol.41 , pp. 579-584
    • Thomas, G.1
  • 39
    • 34250002140 scopus 로고    scopus 로고
    • Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer
    • Stacey, S.N. et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat. Genet. 39, 865-869 (2007).
    • (2007) Nat. Genet. , vol.39 , pp. 865-869
    • Stacey, S.N.1
  • 40
    • 84875703379 scopus 로고    scopus 로고
    • Large-scale genotyping identifies 41 new loci associated with breast cancer risk
    • Michailidou, K. et al. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Nat. Genet. 45, 353-361 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 353-361
    • Michailidou, K.1
  • 41
    • 77952887426 scopus 로고    scopus 로고
    • Genome-wide association study identifies five new breast cancer susceptibility loci
    • Turnbull, C. et al. Genome-wide association study identifies five new breast cancer susceptibility loci. Nat. Genet. 42, 504-507 (2010).
    • (2010) Nat. Genet. , vol.42 , pp. 504-507
    • Turnbull, C.1
  • 42
    • 79957860523 scopus 로고    scopus 로고
    • A combined analysis of genome-wide association studies in breast cancer
    • Li, J. et al. A combined analysis of genome-wide association studies in breast cancer. Breast Cancer Res. Treat. 126, 717-727 (2011).
    • (2011) Breast Cancer Res. Treat. , vol.126 , pp. 717-727
    • Li, J.1
  • 44
    • 84875530540 scopus 로고    scopus 로고
    • LNCipedia: A database for annotated human lncRNA transcript sequences and structures
    • Volders, P.J. et al. LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res. 41, D246-D251 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D246-D251
    • Volders, P.J.1
  • 45
    • 84907032373 scopus 로고    scopus 로고
    • lncRNAtor: A comprehensive resource for functional investigation of long noncoding RNAs
    • Park, C., Yu, N., Choi, I., Kim, W. & Lee, S. lncRNAtor: a comprehensive resource for functional investigation of long noncoding RNAs. Bioinformatics 30, 2480-2485 (2014).
    • (2014) Bioinformatics , vol.30 , pp. 2480-2485
    • Park, C.1    Yu, N.2    Choi, I.3    Kim, W.4    Lee, S.5
  • 46
    • 84879671055 scopus 로고    scopus 로고
    • Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs
    • Hangauer, M.J., Vaughn, I.W. & McManus, M.T. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet. 9, e1003569 (2013).
    • (2013) PLoS Genet. , vol.9
    • Hangauer, M.J.1    Vaughn, I.W.2    McManus, M.T.3
  • 47
    • 34548304069 scopus 로고    scopus 로고
    • Activation of p53 by MEG3 non-coding RNA
    • Zhou, Y. et al. Activation of p53 by MEG3 non-coding RNA. J. Biol. Chem. 282, 24731-24742 (2007).
    • (2007) J. Biol. Chem. , vol.282 , pp. 24731-24742
    • Zhou, Y.1
  • 48
    • 79961222799 scopus 로고    scopus 로고
    • Urine TMPRSS2:ERG fusion transcript stratifies prostate cancer risk in men with elevated serum PSA
    • 94ra72
    • Tomlins, S.A. et al. Urine TMPRSS2:ERG fusion transcript stratifies prostate cancer risk in men with elevated serum PSA. Sci. Transl. Med. 3, 94ra72 (2011).
    • (2011) Sci. Transl. Med. , vol.3
    • Tomlins, S.A.1
  • 49
    • 84896524997 scopus 로고    scopus 로고
    • PCAT-1, a long noncoding RNA, regulates BRCA2 and controls homologous recombination in cancer
    • Prensner, J.R. et al. PCAT-1, a long noncoding RNA, regulates BRCA2 and controls homologous recombination in cancer. Cancer Res. 74, 1651-1660 (2014).
    • (2014) Cancer Res. , vol.74 , pp. 1651-1660
    • Prensner, J.R.1
  • 50
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578 (2012).
    • (2012) Nat. Protoc. , vol.7 , pp. 562-578
    • Trapnell, C.1
  • 51
    • 0020480512 scopus 로고
    • Recognition of protein coding regions in DNA sequences
    • Fickett, J.W. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10, 5303-5318 (1982).
    • (1982) Nucleic Acids Res. , vol.10 , pp. 5303-5318
    • Fickett, J.W.1
  • 52
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim, M.S. et al. A draft map of the human proteome. Nature 509, 575-581 (2014).
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.S.1
  • 53
    • 84867345063 scopus 로고    scopus 로고
    • A cross-platform toolkit for mass spectrometry and proteomics
    • Chambers, M.C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918-920 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 918-920
    • Chambers, M.C.1
  • 54
    • 84862245279 scopus 로고    scopus 로고
    • Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
    • Ye, J. et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134 (2012).
    • (2012) BMC Bioinformatics , vol.13 , pp. 134
    • Ye, J.1
  • 55
    • 84884416048 scopus 로고    scopus 로고
    • Human housekeeping genes, revisited
    • Eisenberg, E. & Levanon, E.Y. Human housekeeping genes, revisited. Trends Genet. 29, 569-574 (2013).
    • (2013) Trends Genet. , vol.29 , pp. 569-574
    • Eisenberg, E.1    Levanon, E.Y.2
  • 56
    • 19944430797 scopus 로고    scopus 로고
    • Genomic maps and comparative analysis of histone modifications in human and mouse
    • Bernstein, B.E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169-181 (2005).
    • (2005) Cell , vol.120 , pp. 169-181
    • Bernstein, B.E.1
  • 57
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 58
    • 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. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 511-515
    • Trapnell, C.1
  • 59
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 60
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni, J.C., Mason, C.E., Mane, S.M., Stephens, M. & Gilad, Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18, 1509-1517 (2008).
    • (2008) Genome Res. , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 61
    • 79958135926 scopus 로고    scopus 로고
    • Molecular signatures database (MSigDB) 3.0
    • Liberzon, A. et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics 27, 1739-1740 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1739-1740
    • Liberzon, A.1


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