메뉴 건너뛰기




Volumn 2015, Issue , 2015, Pages

Predicting the functions of long noncoding RNAs using RNA-seq based on Bayesian network

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; RNA; TRANSCRIPTOME;

EID: 84924560209     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2015/839590     Document Type: Article
Times cited : (20)

References (150)
  • 1
    • 77957243921 scopus 로고    scopus 로고
    • Long noncoding RNAs with enhancer-like function in human cells
    • U. A. Ørom, T. Derrien, M. Beringer et al., "Long noncoding RNAs with enhancer-like function in human cells," Cell, vol. 143, no. 1, pp. 46-58, 2010.
    • (2010) Cell , vol.143 , Issue.1 , pp. 46-58
    • Ørom, U.A.1    Derrien, T.2    Beringer, M.3
  • 2
    • 60149099385 scopus 로고    scopus 로고
    • Evolution and functions of long noncoding RNAs
    • C. P. Ponting, P. L. Oliver, and W. Reik, "Evolution and functions of long noncoding RNAs," Cell, vol. 136, no. 4, pp. 629-641, 2009.
    • (2009) Cell , vol.136 , Issue.4 , pp. 629-641
    • Ponting, C.P.1    Oliver, P.L.2    Reik, W.3
  • 3
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • Y. Hayashizaki, "The transcriptional landscape of the mammalian genome," Science, vol. 309, no. 5740, pp. 1559-1563, 2005.
    • (2005) Science , vol.309 , Issue.5740 , pp. 1559-1563
    • Hayashizaki, Y.1
  • 4
    • 22244442468 scopus 로고    scopus 로고
    • Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    • P. Kapranov, J. Drenkow, J. Cheng et al., "Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays," Genome Research, vol. 15, no. 7, pp. 987-997, 2005.
    • (2005) Genome Research , vol.15 , Issue.7 , pp. 987-997
    • Kapranov, P.1    Drenkow, J.2    Cheng, J.3
  • 5
    • 34250729138 scopus 로고    scopus 로고
    • Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    • J. L. Rinn, M. Kertesz, J. K. Wang et al., "Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs," Cell, vol. 129, no. 7, pp. 1311-1323, 2007.
    • (2007) Cell , vol.129 , Issue.7 , pp. 1311-1323
    • Rinn, J.L.1    Kertesz, M.2    Wang, J.K.3
  • 6
    • 79955586226 scopus 로고    scopus 로고
    • Long noncoding RNAs: The search for function
    • M. Baker, "Long noncoding RNAs: the search for function," Nature Methods, vol. 8, no. 5, pp. 379-383, 2011.
    • (2011) Nature Methods , vol.8 , Issue.5 , pp. 379-383
    • Baker, M.1
  • 7
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • M. Guttman and J. L. Rinn, "Modular regulatory principles of large non-coding RNAs," Nature, vol. 482, no. 7385, pp. 339-346, 2012.
    • (2012) Nature , vol.482 , Issue.7385 , pp. 339-346
    • Guttman, M.1    Rinn, J.L.2
  • 8
    • 80052869283 scopus 로고    scopus 로고
    • LincRNAs act in the circuitry controlling pluripotency and differentiation
    • M. Guttman, J. Donaghey, B. W. Carey et al., "LincRNAs act in the circuitry controlling pluripotency and differentiation," Nature, vol. 477, no. 7364, pp. 295-300, 2011.
    • (2011) Nature , vol.477 , Issue.7364 , pp. 295-300
    • Guttman, M.1    Donaghey, J.2    Carey, B.W.3
  • 9
    • 84455206362 scopus 로고    scopus 로고
    • Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
    • I. Ulitsky, A. Shkumatava, C. H. Jan, H. Sive, and D. P. Bartel, "Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution," Cell, vol. 147, no. 7, pp. 1537-1550, 2011.
    • (2011) Cell , vol.147 , Issue.7 , pp. 1537-1550
    • Ulitsky, I.1    Shkumatava, A.2    Jan, C.H.3    Sive, H.4    Bartel, D.P.5
  • 11
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • M. N. Cabili, C. Trapnell, L. Goff et al., "Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses," Genes & Development, vol. 25, no. 18, pp. 1915-1927, 2011.
    • (2011) Genes & Development , vol.25 , Issue.18 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3
  • 12
    • 84915735396 scopus 로고    scopus 로고
    • Identification of cancer-related lncR-NAs through integrating genome, regulome and transcriptome features
    • T. Zhao, J. Xu, L. Liu et al., "Identification of cancer-related lncR-NAs through integrating genome, regulome and transcriptome features," Molecular BioSystems, vol. 11, no. 1, pp. 126-136, 2015.
    • (2015) Molecular BioSystems , vol.11 , Issue.1 , pp. 126-136
    • Zhao, T.1    Xu, J.2    Liu, L.3
  • 13
    • 84867073340 scopus 로고    scopus 로고
    • Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage
    • J. A. Wamstad, J. M. Alexander, R. M. Truty et al., "Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage," Cell, vol. 151, no. 1, pp. 206-220, 2012.
    • (2012) Cell , vol.151 , Issue.1 , pp. 206-220
    • Wamstad, J.A.1    Alexander, J.M.2    Truty, R.M.3
  • 14
    • 80053045739 scopus 로고    scopus 로고
    • Molecular mechanisms of long noncoding RNAs
    • K. C. Wang and H. Y. Chang, "Molecular mechanisms of long noncoding RNAs," Molecular Cell, vol. 43, no. 6, pp. 904-914, 2011.
    • (2011) Molecular Cell , vol.43 , Issue.6 , pp. 904-914
    • Wang, K.C.1    Chang, H.Y.2
  • 15
    • 84856255316 scopus 로고    scopus 로고
    • Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis
    • L. da Sacco, A. Baldassarre, and A. Masotti, "Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis," International Journal of Molecular Sciences, vol. 13, no. 1, pp. 97-114, 2012.
    • (2012) International Journal of Molecular Sciences , vol.13 , Issue.1 , pp. 97-114
    • Da Sacco, L.1    Baldassarre, A.2    Masotti, A.3
  • 16
    • 84964247754 scopus 로고    scopus 로고
    • Computational identification of epigenetically regulated lncRNAs and their associated genes based on integrating genomic data
    • T. Zhao, J. Xu, L. Liu et al., "Computational identification of epigenetically regulated lncRNAs and their associated genes based on integrating genomic data," FEBS Letters, vol. 589, no. 4, pp. 521-531, 2015.
    • (2015) FEBS Letters , vol.589 , Issue.4 , pp. 521-531
    • Zhao, T.1    Xu, J.2    Liu, L.3
  • 17
    • 79956306617 scopus 로고    scopus 로고
    • Regulation of X-chromosome inactivation by the X-inactivation centre
    • S. Augui, E. P. Nora, and E. Heard, "Regulation of X-chromosome inactivation by the X-inactivation centre," Nature Reviews Genetics, vol. 12, no. 6, pp. 429-442, 2011.
    • (2011) Nature Reviews Genetics , vol.12 , Issue.6 , pp. 429-442
    • Augui, S.1    Nora, E.P.2    Heard, E.3
  • 18
    • 84870478335 scopus 로고    scopus 로고
    • Prioritizing cancer-related key miRNA-target interactions by integrative genomics
    • Y. Xiao, J. Guan, Y. Ping et al., "Prioritizing cancer-related key miRNA-target interactions by integrative genomics," Nucleic Acids Research, vol. 40, no. 16, pp. 7653-7665, 2012.
    • (2012) Nucleic Acids Research , vol.40 , Issue.16 , pp. 7653-7665
    • Xiao, Y.1    Guan, J.2    Ping, Y.3
  • 19
    • 84859211025 scopus 로고    scopus 로고
    • Combined RNAi and localization for functionally dissecting long noncoding RNAs
    • D. Chakraborty, D. Kappei, M. Theis et al., "Combined RNAi and localization for functionally dissecting long noncoding RNAs," Nature Methods, vol. 9, no. 4, pp. 360-362, 2012.
    • (2012) Nature Methods , vol.9 , Issue.4 , pp. 360-362
    • Chakraborty, D.1    Kappei, D.2    Theis, M.3
  • 20
    • 79957840868 scopus 로고    scopus 로고
    • Predicting protein associations with long noncoding RNAs
    • M. Bellucci, F. Agostini, M. Masin, and G. G. Tartaglia, "Predicting protein associations with long noncoding RNAs," Nature Methods, vol. 8, no. 6, pp. 444-445, 2011.
    • (2011) Nature Methods , vol.8 , Issue.6 , pp. 444-445
    • Bellucci, M.1    Agostini, F.2    Masin, M.3    Tartaglia, G.G.4
  • 21
    • 84860575639 scopus 로고    scopus 로고
    • Genome-wide determination of RNA stability reveals hundreds of short-lived non-coding transcripts in mammals
    • H. Tani, R. Mizutani, K. A. Salam et al., "Genome-wide determination of RNA stability reveals hundreds of short-lived non-coding transcripts in mammals," Genome Research, vol. 22, no. 5, pp. 947-956, 2012.
    • (2012) Genome Research , vol.22 , Issue.5 , pp. 947-956
    • Tani, H.1    Mizutani, R.2    Salam, K.A.3
  • 22
    • 84860581983 scopus 로고    scopus 로고
    • Genomewide analysis of long noncoding RNA stability
    • M. B. Clark, R. L. Johnston, M. Inostroza-Ponta et al., "Genomewide analysis of long noncoding RNA stability," Genome Research, vol. 22, no. 5, pp. 885-898, 2012.
    • (2012) Genome Research , vol.22 , Issue.5 , pp. 885-898
    • Clark, M.B.1    Johnston, R.L.2    Inostroza-Ponta, M.3
  • 23
    • 79956010263 scopus 로고    scopus 로고
    • Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network
    • Q. Liao, C. Liu, X. Yuan et al., "Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network," Nucleic Acids Research, vol. 39, no. 9, pp. 3864-3878, 2011.
    • (2011) Nucleic Acids Research , vol.39 , Issue.9 , pp. 3864-3878
    • Liao, Q.1    Liu, C.2    Yuan, X.3
  • 24
    • 55349108569 scopus 로고    scopus 로고
    • Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization
    • S. Flibotte and D. G. Moerman, "Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization," BMC Genomics, vol. 9, article 497, 2008.
    • (2008) BMC Genomics , vol.9
    • Flibotte, S.1    Moerman, D.G.2
  • 25
    • 77951596386 scopus 로고    scopus 로고
    • Large scale analysis of positional effects of single-base mismatches on microarray gene expression data
    • F. Duan, M. A. Pauley, E. R. Spindel, L. Zhang, and R. B. Norgren Jr., "Large scale analysis of positional effects of single-base mismatches on microarray gene expression data," BioData Mining, vol. 3, no. 1, article 2, 2010.
    • (2010) BioData Mining , vol.3 , Issue.1
    • Duan, F.1    Pauley, M.A.2    Spindel, E.R.3    Zhang, L.4    Norgren, R.B.5
  • 26
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, "Mapping and quantifying mammalian transcriptomes by RNA-Seq," Nature Methods, vol. 5, no. 7, pp. 621-628, 2008.
    • (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
  • 27
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Z. Wang, M. Gerstein, and M. Snyder, "RNA-Seq: a revolutionary tool for transcriptomics," Nature Reviews Genetics, vol. 10, no. 1, pp. 57-63, 2009.
    • (2009) Nature Reviews Genetics , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 28
    • 84857836107 scopus 로고    scopus 로고
    • Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    • A. Pauli, E. Valen, M. F. Lin et al., "Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis," Genome Research, vol. 22, no. 3, pp. 577-591, 2012.
    • (2012) Genome Research , vol.22 , Issue.3 , pp. 577-591
    • Pauli, A.1    Valen, E.2    Lin, M.F.3
  • 29
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: The reference human genome annotation for the ENCODE project
    • J. Harrow, A. Frankish, J. M. Gonzalez et al., "GENCODE: the reference human genome annotation for the ENCODE project," Genome Research, vol. 22, no. 9, pp. 1760-1774, 2012.
    • (2012) Genome Research , vol.22 , Issue.9 , pp. 1760-1774
    • Harrow, J.1    Frankish, A.2    Gonzalez, J.M.3
  • 31
    • 79961202865 scopus 로고    scopus 로고
    • Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
    • J. R. Prensner, M. K. Iyer, O. A. Balbin et al., "Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression," Nature Biotechnology, vol. 29, no. 8, pp. 742-749, 2011.
    • (2011) Nature Biotechnology , vol.29 , Issue.8 , pp. 742-749
    • Prensner, J.R.1    Iyer, M.K.2    Balbin, O.A.3
  • 33
    • 84891437638 scopus 로고    scopus 로고
    • An integrated model of the transcriptome of HER2-positive breast cancer
    • K. R. Kalari, B. M. Necela, X. Tang et al., "An integrated model of the transcriptome of HER2-positive breast cancer," PLoS ONE, vol. 8, no. 11, Article ID e79298, 2013.
    • (2013) PLoS ONE , vol.8 , Issue.11
    • Kalari, K.R.1    Necela, B.M.2    Tang, X.3
  • 34
    • 84899733036 scopus 로고    scopus 로고
    • The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder
    • Y. Xiao, C. Camarillo, Y. Ping et al., "The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder," PLoS ONE, vol. 9, no. 4, Article ID e95875, 2014.
    • (2014) PLoS ONE , vol.9 , Issue.4
    • Xiao, Y.1    Camarillo, C.2    Ping, Y.3
  • 35
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • C. Trapnell, L. Pachter, and S. L. Salzberg, "TopHat: discovering splice junctions with RNA-Seq," Bioinformatics, vol. 25, no. 9, pp. 1105-1111, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 36
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • C. Trapnell, B. A. Williams, G. Pertea et al., "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation," Nature Biotechnology, vol. 28, no. 5, pp. 511-515, 2010.
    • (2010) Nature Biotechnology , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3
  • 39
    • 3242891560 scopus 로고    scopus 로고
    • Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection
    • Y. Tamada, S. Kim, H. Bannai et al., "Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection," Bioinformatics, vol. 19, supplement 2, pp. ii227-ii236, 2003.
    • (2003) Bioinformatics , vol.19 , pp. ii227-ii236
    • Tamada, Y.1    Kim, S.2    Bannai, H.3
  • 40
    • 73249118535 scopus 로고    scopus 로고
    • Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy
    • B. Liu, J. Li, A. Tsykin, L. Liu, A. B. Gaur, and G. J. Goodall, "Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy," BMC Bioinformatics, vol. 10, article 408, 2009.
    • (2009) BMC Bioinformatics , vol.10
    • Liu, B.1    Li, J.2    Tsykin, A.3    Liu, L.4    Gaur, A.B.5    Goodall, G.J.6
  • 41
    • 70350690683 scopus 로고    scopus 로고
    • Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data
    • Y. Wang, X.-S. Zhang, and Y. Xia, "Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data," Nucleic Acids Research, vol. 37, no. 18, pp. 5943-5958, 2009.
    • (2009) Nucleic Acids Research , vol.37 , Issue.18 , pp. 5943-5958
    • Wang, Y.1    Zhang, X.-S.2    Xia, Y.3
  • 44
    • 0028482006 scopus 로고
    • Learning Bayesian belief networks: An approach based on the MDL principle
    • W. Lam and F. Bacchus, "Learning Bayesian belief networks: an approach based on the MDL principle," Computational Intelligence, vol. 10, no. 3, pp. 269-293, 1994.
    • (1994) Computational Intelligence , vol.10 , Issue.3 , pp. 269-293
    • Lam, W.1    Bacchus, F.2
  • 45
    • 77955124773 scopus 로고    scopus 로고
    • Learning Bayesian networks with the bnlearn R Package
    • M. Scutari, "Learning Bayesian networks with the bnlearn R Package," Journal of Statistical Software, vol. 35, no. 3, pp. 1-22, 2010.
    • (2010) Journal of Statistical Software , vol.35 , Issue.3 , pp. 1-22
    • Scutari, M.1
  • 46
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • L. H. Hartwell, J. J. Hopfield, S. Leibler, and A. W. Murray, "From molecular to modular cell biology," Nature, vol. 402, supplement, no. 6761, pp. C47-C52, 1999.
    • (1999) Nature , vol.402 , pp. C47-C52
    • Hartwell, L.H.1    Hopfield, J.J.2    Leibler, S.3    Murray, A.W.4
  • 47
    • 33947730844 scopus 로고    scopus 로고
    • Identifying functional modules in the physical interactome of Saccharomyces cerevisiae
    • S. Pu, J. Vlasblom, A. Emili, J. Greenblatt, and S. J. Wodak, "Identifying functional modules in the physical interactome of Saccharomyces cerevisiae," Proteomics, vol. 7, no. 6, pp. 944-960, 2007.
    • (2007) Proteomics , vol.7 , Issue.6 , pp. 944-960
    • Pu, S.1    Vlasblom, J.2    Emili, A.3    Greenblatt, J.4    Wodak, S.J.5
  • 48
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • A. J. Enright, S. van Dongen, and C. A. Ouzounis, "An efficient algorithm for large-scale detection of protein families," Nucleic Acids Research, vol. 30, no. 7, pp. 1575-1584, 2002.
    • (2002) Nucleic Acids Research , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 49
    • 40049099114 scopus 로고    scopus 로고
    • Defining clusters from a hierarchical cluster tree: The Dynamic Tree Cut package for R
    • P. Langfelder, B. Zhang, and S. Horvath, "Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R," Bioinformatics, vol. 24, no. 5, pp. 719-720, 2008.
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 719-720
    • Langfelder, P.1    Zhang, B.2    Horvath, S.3
  • 50
  • 51
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • R. Sharan, I. Ulitsky, and R. Shamir, "Network-based prediction of protein function," Molecular Systems Biology, vol. 3, no. 1, article 88, 2007.
    • (2007) Molecular Systems Biology , vol.3 , Issue.1
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 52
    • 33747344944 scopus 로고    scopus 로고
    • Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
    • I. B. Jeffery, D. G. Higgins, and A. C. Culhane, "Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data," BMC Bioinformatics, vol. 7, article 359, 2006.
    • (2006) BMC Bioinformatics , vol.7
    • Jeffery, I.B.1    Higgins, D.G.2    Culhane, A.C.3
  • 53
    • 79957840356 scopus 로고    scopus 로고
    • Long noncoding RNAs and human disease
    • O. Wapinski and H. Y. Chang, "Long noncoding RNAs and human disease," Trends in Cell Biology, vol. 21, no. 6, pp. 354-361, 2011.
    • (2011) Trends in Cell Biology , vol.21 , Issue.6 , pp. 354-361
    • Wapinski, O.1    Chang, H.Y.2
  • 54
    • 84884673330 scopus 로고    scopus 로고
    • The prostate cancer-up-regulated long noncoding RNA PlncRNA-1 modulates apoptosis and proliferation through reciprocal regulation of androgen receptor
    • Z. Cui, S. Ren, J. Lu et al., "The prostate cancer-up-regulated long noncoding RNA PlncRNA-1 modulates apoptosis and proliferation through reciprocal regulation of androgen receptor," Urologic Oncology: Seminars and Original Investigations, vol. 31, no. 7, pp. 1117-1123, 2013.
    • (2013) Urologic Oncology: Seminars and Original Investigations , vol.31 , Issue.7 , pp. 1117-1123
    • Cui, Z.1    Ren, S.2    Lu, J.3
  • 55
    • 30544452875 scopus 로고    scopus 로고
    • Notch signaling is required for normal prostatic epithelial cell proliferation and differentiation
    • X.-D. Wang, C. C. Leow, J. Zha et al., "Notch signaling is required for normal prostatic epithelial cell proliferation and differentiation," Developmental Biology, vol. 290, no. 1, pp. 66-80, 2006.
    • (2006) Developmental Biology , vol.290 , Issue.1 , pp. 66-80
    • Wang, X.-D.1    Leow, C.C.2    Zha, J.3
  • 56
    • 84864033675 scopus 로고    scopus 로고
    • Malat1 is not an essential component of nuclear speckles in mice
    • S. Nakagawa, J. Y. Ip, G. Shioi et al., "Malat1 is not an essential component of nuclear speckles in mice," RNA, vol. 18, no. 8, pp. 1487-1499, 2012.
    • (2012) RNA , vol.18 , Issue.8 , pp. 1487-1499
    • Nakagawa, S.1    Ip, J.Y.2    Shioi, G.3
  • 58
    • 77956882723 scopus 로고    scopus 로고
    • A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression
    • D. Bernard, K. V. Prasanth, V. Tripathi et al., "A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression," The EMBO Journal, vol. 29, no. 18, pp. 3082-3093, 2010.
    • (2010) The EMBO Journal , vol.29 , Issue.18 , pp. 3082-3093
    • Bernard, D.1    Prasanth, K.V.2    Tripathi, V.3
  • 59
    • 77956927823 scopus 로고    scopus 로고
    • The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation
    • V. Tripathi, J. D. Ellis, Z. Shen et al., "The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation," Molecular Cell, vol. 39, no. 6, pp. 925-938, 2010.
    • (2010) Molecular Cell , vol.39 , Issue.6 , pp. 925-938
    • Tripathi, V.1    Ellis, J.D.2    Shen, Z.3
  • 60
    • 84864315112 scopus 로고    scopus 로고
    • The lncRNA malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult
    • B. Zhang, G. Arun, Y. S. Mao et al., "The lncRNA malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult," Cell Reports, vol. 2, no. 1, pp. 111-123, 2012.
    • (2012) Cell Reports , vol.2 , Issue.1 , pp. 111-123
    • Zhang, B.1    Arun, G.2    Mao, Y.S.3
  • 62
    • 76649122999 scopus 로고    scopus 로고
    • Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation
    • T. R. Mercer, I. A. Qureshi, S. Gokhan et al., "Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation," BMC Neuroscience, vol. 11, article 14, 2010.
    • (2010) BMC Neuroscience , vol.11
    • Mercer, T.R.1    Qureshi, I.A.2    Gokhan, S.3
  • 63
    • 61849113891 scopus 로고    scopus 로고
    • Men ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
    • H. Sunwoo, M. E. Dinger, J. E. Wilusz, P. P. Amaral, J. S. Mattick, and D. L. Spector, "Men ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles," Genome Research, vol. 19, no. 3, pp. 347-359, 2009.
    • (2009) Genome Research , vol.19 , Issue.3 , pp. 347-359
    • Sunwoo, H.1    Dinger, M.E.2    Wilusz, J.E.3    Amaral, P.P.4    Mattick, J.S.5    Spector, D.L.6
  • 64
    • 68949212914 scopus 로고    scopus 로고
    • Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear noncoding RNA
    • L.-L. Chen and G. G. Carmichael, "Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA," Molecular Cell, vol. 35, no. 4, pp. 467-478, 2009.
    • (2009) Molecular Cell , vol.35 , Issue.4 , pp. 467-478
    • Chen, L.-L.1    Carmichael, G.G.2
  • 65
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • M. Guttman, I. Amit, M. Garber et al., "Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals," Nature, vol. 458, no. 7235, pp. 223-227, 2009.
    • (2009) Nature , vol.458 , Issue.7235 , pp. 223-227
    • Guttman, M.1    Amit, I.2    Garber, M.3
  • 66
    • 33750452339 scopus 로고    scopus 로고
    • Abnormal skin, limb and craniofacial morphogenesis in mice deficient for interferon regulatory factor 6 (Irf6)
    • C. R. Ingraham, A. Kinoshita, S. Kondo et al., "Abnormal skin, limb and craniofacial morphogenesis in mice deficient for interferon regulatory factor 6 (Irf6)," Nature Genetics, vol. 38, no. 11, pp. 1335-1340, 2006.
    • (2006) Nature Genetics , vol.38 , Issue.11 , pp. 1335-1340
    • Ingraham, C.R.1    Kinoshita, A.2    Kondo, S.3
  • 67
    • 77951865156 scopus 로고    scopus 로고
    • A regulatory feedback loop involving p63 and IRF6 links the pathogenesis of 2 genetically different human ectodermal dysplasias
    • F. Moretti, B. Marinari, N. L. Iacono et al., "A regulatory feedback loop involving p63 and IRF6 links the pathogenesis of 2 genetically different human ectodermal dysplasias," The Journal of Clinical Investigation, vol. 120, no. 5, pp. 1570-1577, 2010.
    • (2010) The Journal of Clinical Investigation , vol.120 , Issue.5 , pp. 1570-1577
    • Moretti, F.1    Marinari, B.2    Iacono, N.L.3
  • 68
    • 41149129204 scopus 로고    scopus 로고
    • Interferon regulatory factor 6 promotes cell cycle arrest and is regulated by the proteasome in a cell cycle-dependent manner
    • C. M. Bailey, D. E. Abbott, N. V. Margaryan, Z. Khalkhali-Ellis, and M. J. C. Hendrix, "Interferon regulatory factor 6 promotes cell cycle arrest and is regulated by the proteasome in a cell cycle-dependent manner," Molecular and Cellular Biology, vol. 28, no. 7, pp. 2235-2243, 2008.
    • (2008) Molecular and Cellular Biology , vol.28 , Issue.7 , pp. 2235-2243
    • Bailey, C.M.1    Abbott, D.E.2    Margaryan, N.V.3    Khalkhali-Ellis, Z.4    Hendrix, M.J.C.5
  • 69
    • 79960398834 scopus 로고    scopus 로고
    • 2+ concentration, Slc39 (ZiP), and metallothionein gene expression in primary pancreatic islet β-cells
    • 2+ concentration, Slc39 (ZiP), and metallothionein gene expression in primary pancreatic islet β-cells," The Journal of Biological Chemistry, vol. 286, no. 29, pp. 25778-25789, 2011.
    • (2011) The Journal of Biological Chemistry , vol.286 , Issue.29 , pp. 25778-25789
    • Bellomo, E.A.1    Meur, G.2    Rutter, G.A.3
  • 70
    • 0037379164 scopus 로고    scopus 로고
    • The LZT proteins; the LIV-1 subfamily of zinc transporters
    • K. M. Taylor and R. I. Nicholson, "The LZT proteins; the LIV-1 subfamily of zinc transporters," Biochimica et Biophysica Acta - Biomembranes, vol. 1611, no. 1-2, pp. 16-30, 2003.
    • (2003) Biochimica et Biophysica Acta - Biomembranes , vol.1611 , Issue.1-2 , pp. 16-30
    • Taylor, K.M.1    Nicholson, R.I.2
  • 71
    • 84872135457 scopus 로고    scopus 로고
    • Control of somatic tissue differentiation by the long non-coding RNA TINCR
    • M. Kretz, Z. Siprashvili, C. Chu et al., "Control of somatic tissue differentiation by the long non-coding RNA TINCR," Nature, vol. 493, no. 7431, pp. 231-235, 2013.
    • (2013) Nature , vol.493 , Issue.7431 , pp. 231-235
    • Kretz, M.1    Siprashvili, Z.2    Chu, C.3
  • 72
    • 84875417100 scopus 로고    scopus 로고
    • Long non-coding RNAs function annotation: A global prediction method based on bi-colored networks
    • X. Guo, L. Gao, Q. Liao et al., "Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks," Nucleic Acids Research, vol. 41, no. 2, article e35, 2013.
    • (2013) Nucleic Acids Research , vol.41 , Issue.2
    • Guo, X.1    Gao, L.2    Liao, Q.3
  • 73
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • T. Derrien, R. Johnson, G. Bussotti et al., "The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression," Genome Research, vol. 22, no. 9, pp. 1775-1789, 2012.
    • (2012) Genome Research , vol.22 , Issue.9 , pp. 1775-1789
    • Derrien, T.1    Johnson, R.2    Bussotti, G.3
  • 74
    • 84875814497 scopus 로고    scopus 로고
    • Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge
    • S.-Q. Wang and H.-X. Li, "Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge," BMC Systems Biology, vol. 6, no. 1, article S3, 2012.
    • (2012) BMC Systems Biology , vol.6 , Issue.1
    • Wang, S.-Q.1    Li, H.-X.2
  • 75
    • 77955110979 scopus 로고    scopus 로고
    • Genome-wide computational identification and manual annotation of human long noncoding RNA genes
    • H. Jia, M. Osak, G. K. Bogu, L. W. Stanton, R. Johnson, and L. Lipovich, "Genome-wide computational identification and manual annotation of human long noncoding RNA genes," RNA, vol. 16, no. 8, pp. 1478-1487, 2010.
    • (2010) RNA , vol.16 , Issue.8 , pp. 1478-1487
    • Jia, H.1    Osak, M.2    Bogu, G.K.3    Stanton, L.W.4    Johnson, R.5    Lipovich, L.6
  • 76
    • 77957243921 scopus 로고    scopus 로고
    • Long noncoding RNAs with enhancer-like function in human cells
    • U. A. Ørom, T. Derrien, M. Beringer et al., "Long noncoding RNAs with enhancer-like function in human cells," Cell, vol. 143, no. 1, pp. 46-58, 2010.
    • (2010) Cell , vol.143 , Issue.1 , pp. 46-58
    • Ørom, U.A.1    Derrien, T.2    Beringer, M.3
  • 77
    • 60149099385 scopus 로고    scopus 로고
    • Evolution and functions of long noncoding RNAs
    • C. P. Ponting, P. L. Oliver, and W. Reik, "Evolution and functions of long noncoding RNAs," Cell, vol. 136, no. 4, pp. 629-641, 2009.
    • (2009) Cell , vol.136 , Issue.4 , pp. 629-641
    • Ponting, C.P.1    Oliver, P.L.2    Reik, W.3
  • 78
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • Y. Hayashizaki, "The transcriptional landscape of the mammalian genome," Science, vol. 309, no. 5740, pp. 1559-1563, 2005.
    • (2005) Science , vol.309 , Issue.5740 , pp. 1559-1563
    • Hayashizaki, Y.1
  • 79
    • 22244442468 scopus 로고    scopus 로고
    • Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays
    • P. Kapranov, J. Drenkow, J. Cheng et al., "Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays," Genome Research, vol. 15, no. 7, pp. 987-997, 2005.
    • (2005) Genome Research , vol.15 , Issue.7 , pp. 987-997
    • Kapranov, P.1    Drenkow, J.2    Cheng, J.3
  • 80
    • 34250729138 scopus 로고    scopus 로고
    • Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs
    • J. L. Rinn, M. Kertesz, J. K. Wang et al., "Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs," Cell, vol. 129, no. 7, pp. 1311-1323, 2007.
    • (2007) Cell , vol.129 , Issue.7 , pp. 1311-1323
    • Rinn, J.L.1    Kertesz, M.2    Wang, J.K.3
  • 81
    • 79955586226 scopus 로고    scopus 로고
    • Long noncoding RNAs: The search for function
    • M. Baker, "Long noncoding RNAs: the search for function," Nature Methods, vol. 8, no. 5, pp. 379-383, 2011.
    • (2011) Nature Methods , vol.8 , Issue.5 , pp. 379-383
    • Baker, M.1
  • 82
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • M. Guttman and J. L. Rinn, "Modular regulatory principles of large non-coding RNAs," Nature, vol. 482, no. 7385, pp. 339-346, 2012.
    • (2012) Nature , vol.482 , Issue.7385 , pp. 339-346
    • Guttman, M.1    Rinn, J.L.2
  • 83
    • 80052869283 scopus 로고    scopus 로고
    • LincRNAs act in the circuitry controlling pluripotency and differentiation
    • M. Guttman, J. Donaghey, B. W. Carey et al., "LincRNAs act in the circuitry controlling pluripotency and differentiation," Nature, vol. 477, no. 7364, pp. 295-300, 2011.
    • (2011) Nature , vol.477 , Issue.7364 , pp. 295-300
    • Guttman, M.1    Donaghey, J.2    Carey, B.W.3
  • 84
    • 84455206362 scopus 로고    scopus 로고
    • Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution
    • I. Ulitsky, A. Shkumatava, C. H. Jan, H. Sive, and D. P. Bartel, "Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution," Cell, vol. 147, no. 7, pp. 1537-1550, 2011.
    • (2011) Cell , vol.147 , Issue.7 , pp. 1537-1550
    • Ulitsky, I.1    Shkumatava, A.2    Jan, C.H.3    Sive, H.4    Bartel, D.P.5
  • 86
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • M. N. Cabili, C. Trapnell, L. Goff et al., "Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses," Genes & Development, vol. 25, no. 18, pp. 1915-1927, 2011.
    • (2011) Genes & Development , vol.25 , Issue.18 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3
  • 87
    • 84915735396 scopus 로고    scopus 로고
    • Identification of cancer-related lncR-NAs through integrating genome, regulome and transcriptome features
    • T. Zhao, J. Xu, L. Liu et al., "Identification of cancer-related lncR-NAs through integrating genome, regulome and transcriptome features," Molecular BioSystems, vol. 11, no. 1, pp. 126-136, 2015.
    • (2015) Molecular BioSystems , vol.11 , Issue.1 , pp. 126-136
    • Zhao, T.1    Xu, J.2    Liu, L.3
  • 88
    • 84867073340 scopus 로고    scopus 로고
    • Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage
    • J. A. Wamstad, J. M. Alexander, R. M. Truty et al., "Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage," Cell, vol. 151, no. 1, pp. 206-220, 2012.
    • (2012) Cell , vol.151 , Issue.1 , pp. 206-220
    • Wamstad, J.A.1    Alexander, J.M.2    Truty, R.M.3
  • 89
    • 80053045739 scopus 로고    scopus 로고
    • Molecular mechanisms of long noncoding RNAs
    • K. C. Wang and H. Y. Chang, "Molecular mechanisms of long noncoding RNAs," Molecular Cell, vol. 43, no. 6, pp. 904-914, 2011.
    • (2011) Molecular Cell , vol.43 , Issue.6 , pp. 904-914
    • Wang, K.C.1    Chang, H.Y.2
  • 90
    • 84856255316 scopus 로고    scopus 로고
    • Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis
    • L. da Sacco, A. Baldassarre, and A. Masotti, "Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis," International Journal of Molecular Sciences, vol. 13, no. 1, pp. 97-114, 2012.
    • (2012) International Journal of Molecular Sciences , vol.13 , Issue.1 , pp. 97-114
    • Da Sacco, L.1    Baldassarre, A.2    Masotti, A.3
  • 91
    • 84964247754 scopus 로고    scopus 로고
    • Computational identification of epigenetically regulated lncRNAs and their associated genes based on integrating genomic data
    • T. Zhao, J. Xu, L. Liu et al., "Computational identification of epigenetically regulated lncRNAs and their associated genes based on integrating genomic data," FEBS Letters, vol. 589, no. 4, pp. 521-531, 2015.
    • (2015) FEBS Letters , vol.589 , Issue.4 , pp. 521-531
    • Zhao, T.1    Xu, J.2    Liu, L.3
  • 92
    • 79956306617 scopus 로고    scopus 로고
    • Regulation of X-chromosome inactivation by the X-inactivation centre
    • S. Augui, E. P. Nora, and E. Heard, "Regulation of X-chromosome inactivation by the X-inactivation centre," Nature Reviews Genetics, vol. 12, no. 6, pp. 429-442, 2011.
    • (2011) Nature Reviews Genetics , vol.12 , Issue.6 , pp. 429-442
    • Augui, S.1    Nora, E.P.2    Heard, E.3
  • 93
    • 84870478335 scopus 로고    scopus 로고
    • Prioritizing cancer-related key miRNA-target interactions by integrative genomics
    • Y. Xiao, J. Guan, Y. Ping et al., "Prioritizing cancer-related key miRNA-target interactions by integrative genomics," Nucleic Acids Research, vol. 40, no. 16, pp. 7653-7665, 2012.
    • (2012) Nucleic Acids Research , vol.40 , Issue.16 , pp. 7653-7665
    • Xiao, Y.1    Guan, J.2    Ping, Y.3
  • 94
    • 84859211025 scopus 로고    scopus 로고
    • Combined RNAi and localization for functionally dissecting long noncoding RNAs
    • D. Chakraborty, D. Kappei, M. Theis et al., "Combined RNAi and localization for functionally dissecting long noncoding RNAs," Nature Methods, vol. 9, no. 4, pp. 360-362, 2012.
    • (2012) Nature Methods , vol.9 , Issue.4 , pp. 360-362
    • Chakraborty, D.1    Kappei, D.2    Theis, M.3
  • 95
    • 79957840868 scopus 로고    scopus 로고
    • Predicting protein associations with long noncoding RNAs
    • M. Bellucci, F. Agostini, M. Masin, and G. G. Tartaglia, "Predicting protein associations with long noncoding RNAs," Nature Methods, vol. 8, no. 6, pp. 444-445, 2011.
    • (2011) Nature Methods , vol.8 , Issue.6 , pp. 444-445
    • Bellucci, M.1    Agostini, F.2    Masin, M.3    Tartaglia, G.G.4
  • 96
    • 84860575639 scopus 로고    scopus 로고
    • Genome-wide determination of RNA stability reveals hundreds of short-lived non-coding transcripts in mammals
    • H. Tani, R. Mizutani, K. A. Salam et al., "Genome-wide determination of RNA stability reveals hundreds of short-lived non-coding transcripts in mammals," Genome Research, vol. 22, no. 5, pp. 947-956, 2012.
    • (2012) Genome Research , vol.22 , Issue.5 , pp. 947-956
    • Tani, H.1    Mizutani, R.2    Salam, K.A.3
  • 97
    • 84860581983 scopus 로고    scopus 로고
    • Genomewide analysis of long noncoding RNA stability
    • M. B. Clark, R. L. Johnston, M. Inostroza-Ponta et al., "Genomewide analysis of long noncoding RNA stability," Genome Research, vol. 22, no. 5, pp. 885-898, 2012.
    • (2012) Genome Research , vol.22 , Issue.5 , pp. 885-898
    • Clark, M.B.1    Johnston, R.L.2    Inostroza-Ponta, M.3
  • 98
    • 79956010263 scopus 로고    scopus 로고
    • Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network
    • Q. Liao, C. Liu, X. Yuan et al., "Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network," Nucleic Acids Research, vol. 39, no. 9, pp. 3864-3878, 2011.
    • (2011) Nucleic Acids Research , vol.39 , Issue.9 , pp. 3864-3878
    • Liao, Q.1    Liu, C.2    Yuan, X.3
  • 99
    • 55349108569 scopus 로고    scopus 로고
    • Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization
    • S. Flibotte and D. G. Moerman, "Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization," BMC Genomics, vol. 9, article 497, 2008.
    • (2008) BMC Genomics , vol.9
    • Flibotte, S.1    Moerman, D.G.2
  • 100
    • 77951596386 scopus 로고    scopus 로고
    • Large scale analysis of positional effects of single-base mismatches on microarray gene expression data
    • F. Duan, M. A. Pauley, E. R. Spindel, L. Zhang, and R. B. Norgren Jr., "Large scale analysis of positional effects of single-base mismatches on microarray gene expression data," BioData Mining, vol. 3, no. 1, article 2, 2010.
    • (2010) BioData Mining , vol.3 , Issue.1
    • Duan, F.1    Pauley, M.A.2    Spindel, E.R.3    Zhang, L.4    Norgren, R.B.5
  • 101
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-Seq
    • A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, "Mapping and quantifying mammalian transcriptomes by RNA-Seq," Nature Methods, vol. 5, no. 7, pp. 621-628, 2008.
    • (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
  • 102
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Z. Wang, M. Gerstein, and M. Snyder, "RNA-Seq: a revolutionary tool for transcriptomics," Nature Reviews Genetics, vol. 10, no. 1, pp. 57-63, 2009.
    • (2009) Nature Reviews Genetics , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 103
    • 84857836107 scopus 로고    scopus 로고
    • Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
    • A. Pauli, E. Valen, M. F. Lin et al., "Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis," Genome Research, vol. 22, no. 3, pp. 577-591, 2012.
    • (2012) Genome Research , vol.22 , Issue.3 , pp. 577-591
    • Pauli, A.1    Valen, E.2    Lin, M.F.3
  • 104
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: The reference human genome annotation for the ENCODE project
    • J. Harrow, A. Frankish, J. M. Gonzalez et al., "GENCODE: the reference human genome annotation for the ENCODE project," Genome Research, vol. 22, no. 9, pp. 1760-1774, 2012.
    • (2012) Genome Research , vol.22 , Issue.9 , pp. 1760-1774
    • Harrow, J.1    Frankish, A.2    Gonzalez, J.M.3
  • 106
    • 79961202865 scopus 로고    scopus 로고
    • Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
    • J. R. Prensner, M. K. Iyer, O. A. Balbin et al., "Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression," Nature Biotechnology, vol. 29, no. 8, pp. 742-749, 2011.
    • (2011) Nature Biotechnology , vol.29 , Issue.8 , pp. 742-749
    • Prensner, J.R.1    Iyer, M.K.2    Balbin, O.A.3
  • 108
    • 84891437638 scopus 로고    scopus 로고
    • An integrated model of the transcriptome of HER2-positive breast cancer
    • K. R. Kalari, B. M. Necela, X. Tang et al., "An integrated model of the transcriptome of HER2-positive breast cancer," PLoS ONE, vol. 8, no. 11, Article ID e79298, 2013.
    • (2013) PLoS ONE , vol.8 , Issue.11
    • Kalari, K.R.1    Necela, B.M.2    Tang, X.3
  • 109
    • 84899733036 scopus 로고    scopus 로고
    • The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder
    • Y. Xiao, C. Camarillo, Y. Ping et al., "The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder," PLoS ONE, vol. 9, no. 4, Article ID e95875, 2014.
    • (2014) PLoS ONE , vol.9 , Issue.4
    • Xiao, Y.1    Camarillo, C.2    Ping, Y.3
  • 110
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • C. Trapnell, L. Pachter, and S. L. Salzberg, "TopHat: discovering splice junctions with RNA-Seq," Bioinformatics, vol. 25, no. 9, pp. 1105-1111, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 111
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • C. Trapnell, B. A. Williams, G. Pertea et al., "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation," Nature Biotechnology, vol. 28, no. 5, pp. 511-515, 2010.
    • (2010) Nature Biotechnology , vol.28 , Issue.5 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3
  • 114
    • 3242891560 scopus 로고    scopus 로고
    • Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection
    • Y. Tamada, S. Kim, H. Bannai et al., "Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection," Bioinformatics, vol. 19, supplement 2, pp. ii227-ii236, 2003.
    • (2003) Bioinformatics , vol.19 , pp. ii227-ii236
    • Tamada, Y.1    Kim, S.2    Bannai, H.3
  • 115
    • 73249118535 scopus 로고    scopus 로고
    • Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy
    • B. Liu, J. Li, A. Tsykin, L. Liu, A. B. Gaur, and G. J. Goodall, "Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy," BMC Bioinformatics, vol. 10, article 408, 2009.
    • (2009) BMC Bioinformatics , vol.10
    • Liu, B.1    Li, J.2    Tsykin, A.3    Liu, L.4    Gaur, A.B.5    Goodall, G.J.6
  • 116
    • 70350690683 scopus 로고    scopus 로고
    • Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data
    • Y. Wang, X.-S. Zhang, and Y. Xia, "Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data," Nucleic Acids Research, vol. 37, no. 18, pp. 5943-5958, 2009.
    • (2009) Nucleic Acids Research , vol.37 , Issue.18 , pp. 5943-5958
    • Wang, Y.1    Zhang, X.-S.2    Xia, Y.3
  • 119
    • 0028482006 scopus 로고
    • Learning Bayesian belief networks: An approach based on the MDL principle
    • W. Lam and F. Bacchus, "Learning Bayesian belief networks: an approach based on the MDL principle," Computational Intelligence, vol. 10, no. 3, pp. 269-293, 1994.
    • (1994) Computational Intelligence , vol.10 , Issue.3 , pp. 269-293
    • Lam, W.1    Bacchus, F.2
  • 120
    • 77955124773 scopus 로고    scopus 로고
    • Learning Bayesian networks with the bnlearn R Package
    • M. Scutari, "Learning Bayesian networks with the bnlearn R Package," Journal of Statistical Software, vol. 35, no. 3, pp. 1-22, 2010.
    • (2010) Journal of Statistical Software , vol.35 , Issue.3 , pp. 1-22
    • Scutari, M.1
  • 121
    • 0033518234 scopus 로고    scopus 로고
    • From molecular to modular cell biology
    • L. H. Hartwell, J. J. Hopfield, S. Leibler, and A. W. Murray, "From molecular to modular cell biology," Nature, vol. 402, supplement, no. 6761, pp. C47-C52, 1999.
    • (1999) Nature , vol.402 , pp. C47-C52
    • Hartwell, L.H.1    Hopfield, J.J.2    Leibler, S.3    Murray, A.W.4
  • 122
    • 33947730844 scopus 로고    scopus 로고
    • Identifying functional modules in the physical interactome of Saccharomyces cerevisiae
    • S. Pu, J. Vlasblom, A. Emili, J. Greenblatt, and S. J. Wodak, "Identifying functional modules in the physical interactome of Saccharomyces cerevisiae," Proteomics, vol. 7, no. 6, pp. 944-960, 2007.
    • (2007) Proteomics , vol.7 , Issue.6 , pp. 944-960
    • Pu, S.1    Vlasblom, J.2    Emili, A.3    Greenblatt, J.4    Wodak, S.J.5
  • 123
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • A. J. Enright, S. van Dongen, and C. A. Ouzounis, "An efficient algorithm for large-scale detection of protein families," Nucleic Acids Research, vol. 30, no. 7, pp. 1575-1584, 2002.
    • (2002) Nucleic Acids Research , vol.30 , Issue.7 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 124
    • 40049099114 scopus 로고    scopus 로고
    • Defining clusters from a hierarchical cluster tree: The Dynamic Tree Cut package for R
    • P. Langfelder, B. Zhang, and S. Horvath, "Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R," Bioinformatics, vol. 24, no. 5, pp. 719-720, 2008.
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 719-720
    • Langfelder, P.1    Zhang, B.2    Horvath, S.3
  • 125
  • 126
    • 33947252154 scopus 로고    scopus 로고
    • Network-based prediction of protein function
    • R. Sharan, I. Ulitsky, and R. Shamir, "Network-based prediction of protein function," Molecular Systems Biology, vol. 3, no. 1, article 88, 2007.
    • (2007) Molecular Systems Biology , vol.3 , Issue.1
    • Sharan, R.1    Ulitsky, I.2    Shamir, R.3
  • 127
    • 33747344944 scopus 로고    scopus 로고
    • Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
    • I. B. Jeffery, D. G. Higgins, and A. C. Culhane, "Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data," BMC Bioinformatics, vol. 7, article 359, 2006.
    • (2006) BMC Bioinformatics , vol.7
    • Jeffery, I.B.1    Higgins, D.G.2    Culhane, A.C.3
  • 128
    • 79957840356 scopus 로고    scopus 로고
    • Long noncoding RNAs and human disease
    • O. Wapinski and H. Y. Chang, "Long noncoding RNAs and human disease," Trends in Cell Biology, vol. 21, no. 6, pp. 354-361, 2011.
    • (2011) Trends in Cell Biology , vol.21 , Issue.6 , pp. 354-361
    • Wapinski, O.1    Chang, H.Y.2
  • 129
    • 84884673330 scopus 로고    scopus 로고
    • The prostate cancer-up-regulated long noncoding RNA PlncRNA-1 modulates apoptosis and proliferation through reciprocal regulation of androgen receptor
    • Z. Cui, S. Ren, J. Lu et al., "The prostate cancer-up-regulated long noncoding RNA PlncRNA-1 modulates apoptosis and proliferation through reciprocal regulation of androgen receptor," Urologic Oncology: Seminars and Original Investigations, vol. 31, no. 7, pp. 1117-1123, 2013.
    • (2013) Urologic Oncology: Seminars and Original Investigations , vol.31 , Issue.7 , pp. 1117-1123
    • Cui, Z.1    Ren, S.2    Lu, J.3
  • 130
    • 30544452875 scopus 로고    scopus 로고
    • Notch signaling is required for normal prostatic epithelial cell proliferation and differentiation
    • X.-D. Wang, C. C. Leow, J. Zha et al., "Notch signaling is required for normal prostatic epithelial cell proliferation and differentiation," Developmental Biology, vol. 290, no. 1, pp. 66-80, 2006.
    • (2006) Developmental Biology , vol.290 , Issue.1 , pp. 66-80
    • Wang, X.-D.1    Leow, C.C.2    Zha, J.3
  • 131
    • 84864033675 scopus 로고    scopus 로고
    • Malat1 is not an essential component of nuclear speckles in mice
    • S. Nakagawa, J. Y. Ip, G. Shioi et al., "Malat1 is not an essential component of nuclear speckles in mice," RNA, vol. 18, no. 8, pp. 1487-1499, 2012.
    • (2012) RNA , vol.18 , Issue.8 , pp. 1487-1499
    • Nakagawa, S.1    Ip, J.Y.2    Shioi, G.3
  • 133
    • 77956882723 scopus 로고    scopus 로고
    • A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression
    • D. Bernard, K. V. Prasanth, V. Tripathi et al., "A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression," The EMBO Journal, vol. 29, no. 18, pp. 3082-3093, 2010.
    • (2010) The EMBO Journal , vol.29 , Issue.18 , pp. 3082-3093
    • Bernard, D.1    Prasanth, K.V.2    Tripathi, V.3
  • 134
    • 77956927823 scopus 로고    scopus 로고
    • The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation
    • V. Tripathi, J. D. Ellis, Z. Shen et al., "The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation," Molecular Cell, vol. 39, no. 6, pp. 925-938, 2010.
    • (2010) Molecular Cell , vol.39 , Issue.6 , pp. 925-938
    • Tripathi, V.1    Ellis, J.D.2    Shen, Z.3
  • 135
    • 84864315112 scopus 로고    scopus 로고
    • The lncRNA malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult
    • B. Zhang, G. Arun, Y. S. Mao et al., "The lncRNA malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult," Cell Reports, vol. 2, no. 1, pp. 111-123, 2012.
    • (2012) Cell Reports , vol.2 , Issue.1 , pp. 111-123
    • Zhang, B.1    Arun, G.2    Mao, Y.S.3
  • 137
    • 76649122999 scopus 로고    scopus 로고
    • Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation
    • T. R. Mercer, I. A. Qureshi, S. Gokhan et al., "Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation," BMC Neuroscience, vol. 11, article 14, 2010.
    • (2010) BMC Neuroscience , vol.11
    • Mercer, T.R.1    Qureshi, I.A.2    Gokhan, S.3
  • 138
    • 61849113891 scopus 로고    scopus 로고
    • Men ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
    • H. Sunwoo, M. E. Dinger, J. E. Wilusz, P. P. Amaral, J. S. Mattick, and D. L. Spector, "Men ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles," Genome Research, vol. 19, no. 3, pp. 347-359, 2009.
    • (2009) Genome Research , vol.19 , Issue.3 , pp. 347-359
    • Sunwoo, H.1    Dinger, M.E.2    Wilusz, J.E.3    Amaral, P.P.4    Mattick, J.S.5    Spector, D.L.6
  • 139
    • 68949212914 scopus 로고    scopus 로고
    • Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear noncoding RNA
    • L.-L. Chen and G. G. Carmichael, "Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA," Molecular Cell, vol. 35, no. 4, pp. 467-478, 2009.
    • (2009) Molecular Cell , vol.35 , Issue.4 , pp. 467-478
    • Chen, L.-L.1    Carmichael, G.G.2
  • 140
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • M. Guttman, I. Amit, M. Garber et al., "Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals," Nature, vol. 458, no. 7235, pp. 223-227, 2009.
    • (2009) Nature , vol.458 , Issue.7235 , pp. 223-227
    • Guttman, M.1    Amit, I.2    Garber, M.3
  • 141
    • 33750452339 scopus 로고    scopus 로고
    • Abnormal skin, limb and craniofacial morphogenesis in mice deficient for interferon regulatory factor 6 (Irf6)
    • C. R. Ingraham, A. Kinoshita, S. Kondo et al., "Abnormal skin, limb and craniofacial morphogenesis in mice deficient for interferon regulatory factor 6 (Irf6)," Nature Genetics, vol. 38, no. 11, pp. 1335-1340, 2006.
    • (2006) Nature Genetics , vol.38 , Issue.11 , pp. 1335-1340
    • Ingraham, C.R.1    Kinoshita, A.2    Kondo, S.3
  • 142
    • 77951865156 scopus 로고    scopus 로고
    • A regulatory feedback loop involving p63 and IRF6 links the pathogenesis of 2 genetically different human ectodermal dysplasias
    • F. Moretti, B. Marinari, N. L. Iacono et al., "A regulatory feedback loop involving p63 and IRF6 links the pathogenesis of 2 genetically different human ectodermal dysplasias," The Journal of Clinical Investigation, vol. 120, no. 5, pp. 1570-1577, 2010.
    • (2010) The Journal of Clinical Investigation , vol.120 , Issue.5 , pp. 1570-1577
    • Moretti, F.1    Marinari, B.2    Iacono, N.L.3
  • 143
    • 41149129204 scopus 로고    scopus 로고
    • Interferon regulatory factor 6 promotes cell cycle arrest and is regulated by the proteasome in a cell cycle-dependent manner
    • C. M. Bailey, D. E. Abbott, N. V. Margaryan, Z. Khalkhali-Ellis, and M. J. C. Hendrix, "Interferon regulatory factor 6 promotes cell cycle arrest and is regulated by the proteasome in a cell cycle-dependent manner," Molecular and Cellular Biology, vol. 28, no. 7, pp. 2235-2243, 2008.
    • (2008) Molecular and Cellular Biology , vol.28 , Issue.7 , pp. 2235-2243
    • Bailey, C.M.1    Abbott, D.E.2    Margaryan, N.V.3    Khalkhali-Ellis, Z.4    Hendrix, M.J.C.5
  • 144
    • 79960398834 scopus 로고    scopus 로고
    • 2+ concentration, Slc39 (ZiP), and metallothionein gene expression in primary pancreatic islet β-cells
    • 2+ concentration, Slc39 (ZiP), and metallothionein gene expression in primary pancreatic islet β-cells," The Journal of Biological Chemistry, vol. 286, no. 29, pp. 25778-25789, 2011.
    • (2011) The Journal of Biological Chemistry , vol.286 , Issue.29 , pp. 25778-25789
    • Bellomo, E.A.1    Meur, G.2    Rutter, G.A.3
  • 145
    • 0037379164 scopus 로고    scopus 로고
    • The LZT proteins; the LIV-1 subfamily of zinc transporters
    • K. M. Taylor and R. I. Nicholson, "The LZT proteins; the LIV-1 subfamily of zinc transporters," Biochimica et Biophysica Acta - Biomembranes, vol. 1611, no. 1-2, pp. 16-30, 2003.
    • (2003) Biochimica et Biophysica Acta - Biomembranes , vol.1611 , Issue.1-2 , pp. 16-30
    • Taylor, K.M.1    Nicholson, R.I.2
  • 146
    • 84872135457 scopus 로고    scopus 로고
    • Control of somatic tissue differentiation by the long non-coding RNA TINCR
    • M. Kretz, Z. Siprashvili, C. Chu et al., "Control of somatic tissue differentiation by the long non-coding RNA TINCR," Nature, vol. 493, no. 7431, pp. 231-235, 2013.
    • (2013) Nature , vol.493 , Issue.7431 , pp. 231-235
    • Kretz, M.1    Siprashvili, Z.2    Chu, C.3
  • 147
    • 84875417100 scopus 로고    scopus 로고
    • Long non-coding RNAs function annotation: A global prediction method based on bi-colored networks
    • X. Guo, L. Gao, Q. Liao et al., "Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks," Nucleic Acids Research, vol. 41, no. 2, article e35, 2013.
    • (2013) Nucleic Acids Research , vol.41 , Issue.2
    • Guo, X.1    Gao, L.2    Liao, Q.3
  • 148
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • T. Derrien, R. Johnson, G. Bussotti et al., "The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression," Genome Research, vol. 22, no. 9, pp. 1775-1789, 2012.
    • (2012) Genome Research , vol.22 , Issue.9 , pp. 1775-1789
    • Derrien, T.1    Johnson, R.2    Bussotti, G.3
  • 149
    • 84875814497 scopus 로고    scopus 로고
    • Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge
    • S.-Q. Wang and H.-X. Li, "Bayesian inference based modelling for gene transcriptional dynamics by integrating multiple source of knowledge," BMC Systems Biology, vol. 6, no. 1, article S3, 2012.
    • (2012) BMC Systems Biology , vol.6 , Issue.1
    • Wang, S.-Q.1    Li, H.-X.2
  • 150
    • 77955110979 scopus 로고    scopus 로고
    • Genome-wide computational identification and manual annotation of human long noncoding RNA genes
    • H. Jia, M. Osak, G. K. Bogu, L. W. Stanton, R. Johnson, and L. Lipovich, "Genome-wide computational identification and manual annotation of human long noncoding RNA genes," RNA, vol. 16, no. 8, pp. 1478-1487, 2010.
    • (2010) RNA , vol.16 , Issue.8 , pp. 1478-1487
    • Jia, H.1    Osak, M.2    Bogu, G.K.3    Stanton, L.W.4    Johnson, R.5    Lipovich, L.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.