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Volumn 18, Issue 1, 2017, Pages 9-27

Computational recognition for long non-coding RNA (lncRNA): Software and databases

Author keywords

Algorithms; Bioinformatics; Databases; Long non coding RNA

Indexed keywords

LONG UNTRANSLATED RNA;

EID: 85015962248     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbv114     Document Type: Article
Times cited : (37)

References (101)
  • 1
    • 34250189924 scopus 로고    scopus 로고
    • Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription
    • Nakaya H, Amaral P, Louro R, et al. Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol 2007;8:R43.
    • (2007) Genome Biol , vol.8 , pp. R43
    • Nakaya, H.1    Amaral, P.2    Louro, R.3
  • 2
    • 77952905505 scopus 로고    scopus 로고
    • Most "dark matter" transcripts are associated with known genes
    • van Bakel H, Nislow C, Blencowe B, et al. Most "dark matter" transcripts are associated with known genes. PLoS Biol 2010;8:e1000371.
    • (2010) PLoS Biol , vol.8
    • van Bakel, H.1    Nislow, C.2    Blencowe, B.3
  • 3
    • 79960921433 scopus 로고    scopus 로고
    • Response to "The reality of pervasive transcription"
    • van Bakel H, Nislow C, Blencowe B, et al. Response to "The reality of pervasive transcription". PLoS Biol 2011;9:e1001102.
    • (2011) PLoS Biol , vol.9
    • van Bakel, H.1    Nislow, C.2    Blencowe, B.3
  • 4
    • 78651481549 scopus 로고    scopus 로고
    • Transcribed dark matter: meaning or myth?
    • CP P, TG B. Transcribed dark matter: meaning or myth? Hum Mol Genet 2010;19:R162-8.
    • (2010) Hum Mol Genet , vol.19 , pp. R162-R168
    • Ponting, C.P.1    Belgard, T.G.2
  • 5
    • 84860581983 scopus 로고    scopus 로고
    • Genome-wide analysis of long noncoding RNA stability
    • Clark M, Johnston R, Inostroza-Ponta M, et al. Genome-wide analysis of long noncoding RNA stability. Genome Res 2012;22:885-98.
    • (2012) Genome Res , vol.22 , pp. 885-898
    • Clark, M.1    Johnston, R.2    Inostroza-Ponta, M.3
  • 6
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Consortium EP, Dunham I, Kundaje A, et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012;489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
    • Consortium, E.P.1    Dunham, I.2    Kundaje, A.3
  • 7
    • 50649118350 scopus 로고    scopus 로고
    • Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
    • Dinger M, Amaral P, Mercer T, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008;18:1433-45.
    • (2008) Genome Res , vol.18 , pp. 1433-1445
    • Dinger, M.1    Amaral, P.2    Mercer, T.3
  • 9
    • 78651325932 scopus 로고    scopus 로고
    • lncRNAdb: a reference database for long noncoding RNAs
    • Amaral P, Clark M, Gascoigne D, et al. lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 2011;39: D146-51.
    • (2011) Nucleic Acids Res , vol.39 , pp. D146-D151
    • Amaral, P.1    Clark, M.2    Gascoigne, D.3
  • 10
    • 67650474314 scopus 로고    scopus 로고
    • Transcriptional regulation through noncoding RNAs and epigenetic modifications
    • Kurokawa R, Rosenfeld M, Glass C. Transcriptional regulation through noncoding RNAs and epigenetic modifications. RNA Biol 2009;6:233-6.
    • (2009) RNA Biol , vol.6 , pp. 233-236
    • Kurokawa, R.1    Rosenfeld, M.2    Glass, C.3
  • 11
    • 84891759581 scopus 로고    scopus 로고
    • Building non-coding RNA families
    • In:Turner DM (ed). New York City: Humana Press
    • Barquist L, Burge S, Gardner P. Building non-coding RNA families. In: Turner DM (ed). Methods in Molecular BIology. New York City: Humana Press, 2015.
    • (2015) Methods in Molecular BIology
    • Barquist, L.1    Burge, S.2    Gardner, P.3
  • 12
    • 84869052718 scopus 로고    scopus 로고
    • EM. Cis-acting noncoding RNAs: friends and foes
    • Guil S. EM. Cis-acting noncoding RNAs: friends and foes. Nat Structural Mol Biol 2012;19:1068-75.
    • (2012) Nat Structural Mol Biol , vol.19 , pp. 1068-1075
    • Guil, S.1
  • 13
    • 77955501804 scopus 로고    scopus 로고
    • Widely conserved signaling pathways in the establishment of cell polarity
    • McCaffrey L, Macara I. Widely conserved signaling pathways in the establishment of cell polarity. Cold Spring Harb Perspect Biol 2009;1:a001370.
    • (2009) Cold Spring Harb Perspect Biol , vol.1
    • McCaffrey, L.1    Macara, I.2
  • 14
    • 84865727393 scopus 로고    scopus 로고
    • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
    • Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2012;22: 1775-89.
    • (2012) Genome Res , vol.22 , pp. 1775-1789
    • Derrien, T.1    Johnson, R.2    Bussotti, G.3
  • 16
    • 84860742355 scopus 로고    scopus 로고
    • NONCODE v3.0: integrative annotation of long noncoding RNAs
    • Bu D, Yu K, Sun S, et al. NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 2012;40: D210-15.
    • (2012) Nucleic Acids Res , vol.40 , pp. D210-D215
    • Bu, D.1    Yu, K.2    Sun, S.3
  • 17
    • 84875530540 scopus 로고    scopus 로고
    • LNCipedia: a database for annotated human lncRNA transcript sequences and structures
    • Volders PJ, Helsens K, Wang X, et al. LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Res 2013;41:D246-51.
    • (2013) Nucleic Acids Res , vol.41 , pp. D246-D251
    • Volders, P.J.1    Helsens, K.2    Wang, X.3
  • 18
    • 33846056835 scopus 로고    scopus 로고
    • fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
    • Kin T, Yamada K, Terai G, et al. fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res 2007;35:D145-8.
    • (2007) Nucleic Acids Res , vol.35 , pp. D145-D148
    • Kin, T.1    Yamada, K.2    Terai, G.3
  • 19
    • 84947553244 scopus 로고    scopus 로고
    • C-It-Loci: a knowledge database for tissue-enriched loci
    • Weirick T, John D, Dimmeler S, et al. C-It-Loci: a knowledge database for tissue-enriched loci. Bioinformatics 2015;31:3537-43.
    • (2015) Bioinformatics , vol.31 , pp. 3537-3543
    • Weirick, T.1    John, D.2    Dimmeler, S.3
  • 20
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN, Trapnell C, Goff L, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011;25:1915-27.
    • (2011) Genes Dev , vol.25 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3
  • 21
    • 84867603353 scopus 로고    scopus 로고
    • Computational analysis of non-coding RNAs
    • Washietl S, Will S, Hensrix D, et al. Computational analysis of non-coding RNAs. WIRES RNA 2012;3:759-78.
    • (2012) WIRES RNA , vol.3 , pp. 759-778
    • Washietl, S.1    Will, S.2    Hensrix, D.3
  • 22
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • Guttman M, Rinn J. Modular regulatory principles of large non-coding RNAs. Nature 2012;482:339-46.
    • (2012) Nature , vol.482 , pp. 339-346
    • Guttman, M.1    Rinn, J.2
  • 23
    • 56349113455 scopus 로고    scopus 로고
    • 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA
    • Wilusz JE, Freier SM, Spector DL. 3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 2008;135:919-32.
    • (2008) Cell , vol.135 , pp. 919-932
    • Wilusz, J.E.1    Freier, S.M.2    Spector, D.L.3
  • 24
    • 84941702202 scopus 로고    scopus 로고
    • Computational approaches towards understanding human long non-coding RNA biology
    • Jalali S, Kapoor S, Sivadas A, et al. Computational approaches towards understanding human long non-coding RNA biology. Bioinformatics 2015;31:2241-51.
    • (2015) Bioinformatics , vol.31 , pp. 2241-2251
    • Jalali, S.1    Kapoor, S.2    Sivadas, A.3
  • 25
    • 84908123944 scopus 로고    scopus 로고
    • Databases for lncRNAs: a comparative evaluation of emerging tools
    • Fritah S, Niclou S, Azuaje F. Databases for lncRNAs: a comparative evaluation of emerging tools. RNA 2014;20:1655-65.
    • (2014) RNA , vol.20 , pp. 1655-1665
    • Fritah, S.1    Niclou, S.2    Azuaje, F.3
  • 26
    • 62249133709 scopus 로고    scopus 로고
    • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    • Guttman M, Amit I, Garber M, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009;458:223-7.
    • (2009) Nature , vol.458 , pp. 223-227
    • Guttman, M.1    Amit, I.2    Garber, M.3
  • 27
    • 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, Garber M, Levin JZ, et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 2010;28:503-10.
    • (2010) Nat Biotechnol , vol.28 , pp. 503-510
    • Guttman, M.1    Garber, M.2    Levin, J.Z.3
  • 28
    • 80053045739 scopus 로고    scopus 로고
    • Molecular mechanisms of long noncoding RNAs
    • Wang K, Chang H. Molecular mechanisms of long noncoding RNAs. Mol Cell 2011;43:904-14.
    • (2011) Mol Cell , vol.43 , pp. 904-914
    • Wang, K.1    Chang, H.2
  • 29
    • 84875458403 scopus 로고    scopus 로고
    • Charity begins at home: non-coding RNA functions in DNA repair
    • Chowdhury D, Choi YE, Brault ME. Charity begins at home: non-coding RNA functions in DNA repair. Nat Rev Mol Cell Biol 2013;14:181-9.
    • (2013) Nat Rev Mol Cell Biol , vol.14 , pp. 181-189
    • Chowdhury, D.1    Choi, Y.E.2    Brault, M.E.3
  • 30
    • 84893126637 scopus 로고    scopus 로고
    • Transcribed ultraconserved region in human cancers
    • Peng J, Shen J, Ran Z. Transcribed ultraconserved region in human cancers. RNA Biol 2013;10:1771-7.
    • (2013) RNA Biol , vol.10 , pp. 1771-1777
    • Peng, J.1    Shen, J.2    Ran, Z.3
  • 31
    • 77953808788 scopus 로고    scopus 로고
    • An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours
    • Mestdagh P, Fredlund E, Pattyn F, et al. An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours. Oncogene 2010;29:3583-92.
    • (2010) Oncogene , vol.29 , pp. 3583-3592
    • Mestdagh, P.1    Fredlund, E.2    Pattyn, F.3
  • 32
    • 84864033675 scopus 로고    scopus 로고
    • Malat1 is not an essential component of nuclear speckles inmice
    • Nakagawa S, Ip J, Shioi G, et al.Malat1 is not an essential component of nuclear speckles inmice. RNA 2012;18:1487-99.
    • (2012) RNA , vol.18 , pp. 1487-1499
    • Nakagawa, S.1    Ip, J.2    Shioi, G.3
  • 33
    • 4143115768 scopus 로고    scopus 로고
    • Characterization of the splice sites in GT-AG and GC-AG introns
    • Kitamura-Abe S, Itoh H, Washio T, et al. Characterization of the splice sites in GT-AG and GC-AG introns. J Bioinform Comput Biol 2004;2:309-31.
    • (2004) J Bioinform Comput Biol , vol.2 , pp. 309-331
    • Kitamura-Abe, S.1    Itoh, H.2    Washio, T.3
  • 34
    • 84907212706 scopus 로고    scopus 로고
    • LncRBase: An Enriched Resource for lncRNA Information
    • Chakraborty S, Deb A, Maji R, et al. LncRBase: An Enriched Resource for lncRNA Information. PloS One 2014;9:e108010.
    • (2014) PloS One , vol.9
    • Chakraborty, S.1    Deb, A.2    Maji, R.3
  • 35
    • 79956330964 scopus 로고    scopus 로고
    • CpG islands and the regulation of transcription
    • Deaton AM, Bird A. CpG islands and the regulation of transcription. Genes Dev 2011;25:1010-22.
    • (2011) Genes Dev , vol.25 , pp. 1010-1022
    • Deaton, A.M.1    Bird, A.2
  • 36
    • 84938772947 scopus 로고    scopus 로고
    • Emergence, retention and selection: a trilogy of origination for functional de novo proteins from ancestral LncRNAs in primates
    • JY C, QS S, WZ Z, et al. Emergence, retention and selection: a trilogy of origination for functional de novo proteins from ancestral LncRNAs in primates. PLoS Genet 2015;11:e1005391.
    • (2015) PLoS Genet , vol.11
    • Chen, J.-Y.1    Shen, Q.S.2    Zhou, W.-Z.3
  • 37
    • 84869015900 scopus 로고    scopus 로고
    • Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci
    • Sati S, Ghosh S, Jain V, et al. Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. Nucleic Acids Res 2012;40:10018-31.
    • (2012) Nucleic Acids Res , vol.40 , pp. 10018-10031
    • Sati, S.1    Ghosh, S.2    Jain, V.3
  • 38
    • 84928608163 scopus 로고    scopus 로고
    • Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes
    • Su X, Malouf G, Chen Y, et al. Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes. Oncotarget 2014;5:9864-76.
    • (2014) Oncotarget , vol.5 , pp. 9864-9876
    • Su, X.1    Malouf, G.2    Chen, Y.3
  • 39
    • 84906217278 scopus 로고    scopus 로고
    • Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells
    • EL P, RL T, JJ T, et al. Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells. Genome Biol 2014;15:R81.
    • (2014) Genome Biol , vol.15 , pp. R81
    • Putiri, E.L.1    Tiedemann, R.L.2    Thompson, J.J.3
  • 40
    • 84926658082 scopus 로고    scopus 로고
    • Long ncRNA expression associates with tissue-specific enhancers
    • Vučićević D, Corradin O, Ntini E, et al. Long ncRNA expression associates with tissue-specific enhancers. Cell Cycle 2015;14:253-60.
    • (2015) Cell Cycle , vol.14 , pp. 253-260
    • Vučićević, D.1    Corradin, O.2    Ntini, E.3
  • 41
    • 84938866468 scopus 로고    scopus 로고
    • Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin
    • Tsoi L, Iyer M, Stuart P, et al. Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin. Genome Biol 2015;16:24-39.
    • (2015) Genome Biol , vol.16 , pp. 24-39
    • Tsoi, L.1    Iyer, M.2    Stuart, P.3
  • 42
    • 85117313432 scopus 로고    scopus 로고
    • Discovery of protein-lncRNA interactions by integrating large-scale CLIP-seq and RNA-seq datasets
    • Li J, Liu S, Zheng L, et al. Discovery of protein-lncRNA interactions by integrating large-scale CLIP-seq and RNA-seq datasets. Front Bioeng Biotechnol 2015;2:88-99.
    • (2015) Front Bioeng Biotechnol , vol.2 , pp. 88-99
    • Li, J.1    Liu, S.2    Zheng, L.3
  • 43
    • 84936888396 scopus 로고    scopus 로고
    • Design and bioinformatics analysis of genome-wide CLIP experiments
    • Wang T, Xiao G, Chu Y, et al. Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Res 2015;43:5263-74.
    • (2015) Nucleic Acids Res , vol.43 , pp. 5263-5274
    • Wang, T.1    Xiao, G.2    Chu, Y.3
  • 44
    • 84873550059 scopus 로고    scopus 로고
    • Systematic transcriptome wide analysis of lncRNA-miRNA interactions
    • Jalali S, Bhartiya D, Lalwani M, et al. Systematic transcriptome wide analysis of lncRNA-miRNA interactions. PloS One 2013;8:e53823.
    • (2013) PloS One , vol.8
    • Jalali, S.1    Bhartiya, D.2    Lalwani, M.3
  • 45
    • 84856998951 scopus 로고    scopus 로고
    • The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs
    • Wang X, Song X, Glass CK, et al. The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs. Cold Spring Harb Perspect Biol 2011;3: a003756.
    • (2011) Cold Spring Harb Perspect Biol , vol.3
    • Wang, X.1    Song, X.2    Glass, C.K.3
  • 46
    • 84864662896 scopus 로고    scopus 로고
    • Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes
    • Qu Z, Adelson D. Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes. PloS One 2012;7:e42638.
    • (2012) PloS One , vol.7
    • Qu, Z.1    Adelson, D.2
  • 47
    • 84857066786 scopus 로고    scopus 로고
    • Modular regulatory principles of large non-coding RNAs
    • Guttman M, Rinn J. Modular regulatory principles of large non-coding RNAs. Nature 2012;482:339-46.
    • (2012) Nature , vol.482 , pp. 339-346
    • Guttman, M.1    Rinn, J.2
  • 48
    • 79957533104 scopus 로고    scopus 로고
    • Non-coding RNAs as regulators of gene expression and epigenetics
    • Kaikkonen MU, Lam MT, Glass CK. Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc Res 2011;90:430-40.
    • (2011) Cardiovasc Res , vol.90 , pp. 430-440
    • Kaikkonen, M.U.1    Lam, M.T.2    Glass, C.K.3
  • 49
    • 84866529499 scopus 로고    scopus 로고
    • ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins
    • Tempel S, Pollet N, Tahi F. ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins. BMC Bioinformatics 2012;13:246-59.
    • (2012) BMC Bioinformatics , vol.13 , pp. 246-259
    • Tempel, S.1    Pollet, N.2    Tahi, F.3
  • 50
    • 84866295474 scopus 로고    scopus 로고
    • Characterizing ncRNAs in human pathogenic protists using high-throughput sequencing technology
    • Collins LJ. Characterizing ncRNAs in human pathogenic protists using high-throughput sequencing technology. Front Genet 2011;2:96.
    • (2011) Front Genet , vol.2 , pp. 96
    • Collins, L.J.1
  • 51
    • 78651481549 scopus 로고    scopus 로고
    • Transcribed dark matter: meaning or myth?
    • Ponting CP, Belgard TG. Transcribed dark matter: meaning or myth? Hum Mol Genet 2010;19:R162-8.
    • (2010) Hum Mol Genet , vol.19 , pp. R162-R168
    • Ponting, C.P.1    Belgard, T.G.2
  • 52
    • 84976883041 scopus 로고    scopus 로고
    • Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers
    • Ning S, Zhang J, Wang P, et al. Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers. Nucleic Acids Res 2016;44(D1):D980-5.
    • (2016) Nucleic Acids Res , vol.44 , Issue.D1 , pp. D980-D985
    • Ning, S.1    Zhang, J.2    Wang, P.3
  • 53
    • 5044247756 scopus 로고    scopus 로고
    • INCA: synonymous codon usage analysis and clustering by means of self-organizing map
    • Supek F, Vlahovicek K. INCA: synonymous codon usage analysis and clustering by means of self-organizing map. Bioinformatics 2004;20:2329-30.
    • (2004) Bioinformatics , vol.20 , pp. 2329-2330
    • Supek, F.1    Vlahovicek, K.2
  • 55
    • 33751361304 scopus 로고    scopus 로고
    • Inference of splicing regulatory activities by sequence neighborhood analysis
    • Stadler M, Shomron N, Yeo G, et al. Inference of splicing regulatory activities by sequence neighborhood analysis. PLos Genetics 2006;2:e191.
    • (2006) PLos Genetics , vol.2
    • Stadler, M.1    Shomron, N.2    Yeo, G.3
  • 56
    • 70449707788 scopus 로고    scopus 로고
    • The use of covariance models to annotate RNAs in whole genomes
    • Gardner PP. The use of covariance models to annotate RNAs in whole genomes. Brief Funct Genomic Proteomic 2009;8: 444-50.
    • (2009) Brief Funct Genomic Proteomic , vol.8 , pp. 444-450
    • Gardner, P.P.1
  • 57
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy S. Profile hidden Markov models. Bioinformatics 1998;14:755-63.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.1
  • 58
    • 72649102783 scopus 로고    scopus 로고
    • A hidden Markov random field model for genome-wide association studies
    • Li H, Wei Z, Maris J. A hidden Markov random field model for genome-wide association studies. Biostatistics 2010;11:139-50.
    • (2010) Biostatistics , vol.11 , pp. 139-150
    • Li, H.1    Wei, Z.2    Maris, J.3
  • 59
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: interactive sequence similarity searching
    • Finn R, Clements J, Eddy S. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011;39:W29-37.
    • (2011) Nucleic Acids Res , vol.39 , pp. W29-W37
    • Finn, R.1    Clements, J.2    Eddy, S.3
  • 60
    • 0030925920 scopus 로고    scopus 로고
    • Pfam: a comprehensive database of protein domain families based on seed alignments
    • Sonnhammer E, Eddy S, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 1997;28:405-20.
    • (1997) Proteins , vol.28 , pp. 405-420
    • Sonnhammer, E.1    Eddy, S.2    Durbin, R.3
  • 61
    • 1942425486 scopus 로고    scopus 로고
    • Improving profile HMM discrimination by adapting transition probabilities
    • Wistrand M, Sonnhammer EL. Improving profile HMM discrimination by adapting transition probabilities. J Mol Biol 2004;338:847-54.
    • (2004) J Mol Biol , vol.338 , pp. 847-854
    • Wistrand, M.1    Sonnhammer, E.L.2
  • 62
    • 34547582418 scopus 로고    scopus 로고
    • CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
    • Kong L, Zhang Y, Ye Z, et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 2007;35:W345-9.
    • (2007) Nucleic Acids Res , vol.35 , pp. W345-W349
    • Kong, L.1    Zhang, Y.2    Ye, Z.3
  • 63
    • 80053899293 scopus 로고    scopus 로고
    • Complete mitochondrial DNA sequence of the European flat oyster Ostrea edulis confirms Ostreidae classification
    • Danic-Tchaleu G, Heurtebise S, Morga B, et al. Complete mitochondrial DNA sequence of the European flat oyster Ostrea edulis confirms Ostreidae classification. BMC Res Notes 2011;4:400.
    • (2011) BMC Res Notes , vol.4 , pp. 400
    • Danic-Tchaleu, G.1    Heurtebise, S.2    Morga, B.3
  • 64
    • 77949285980 scopus 로고    scopus 로고
    • Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA
    • Doucet-Beaupre H, Breton S, Chapman EG, et al. Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA. BMC Evol Biol 2010;10:50.
    • (2010) BMC Evol Biol , vol.10 , pp. 50
    • Doucet-Beaupre, H.1    Breton, S.2    Chapman, E.G.3
  • 65
    • 84884172494 scopus 로고    scopus 로고
    • Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM
    • Achawanantakun R, Sun Y. Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM. BMC Bioinformatics 2013;14 (Suppl 2):S1.
    • (2013) BMC Bioinformatics , vol.14 , pp. S1
    • Achawanantakun, R.1    Sun, Y.2
  • 66
    • 34547564982 scopus 로고    scopus 로고
    • pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
    • Reeder J, Steffen P, Giegerich R. pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. Nucleic Acids Res 2007;35:W320-4.
    • (2007) Nucleic Acids Res , vol.35 , pp. W320-W324
    • Reeder, J.1    Steffen, P.2    Giegerich, R.3
  • 67
    • 33749377869 scopus 로고    scopus 로고
    • Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
    • Berezikov E, van Tetering G, Verheul M, et al. Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res 2006;16:1289-98.
    • (2006) Genome Res , vol.16 , pp. 1289-1298
    • Berezikov, E.1    van Tetering, G.2    Verheul, M.3
  • 69
    • 84891818924 scopus 로고    scopus 로고
    • starBase v2.0: decoding miRNAceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
    • Li J, Liu S, Zhou H, et al. starBase v2.0: decoding miRNAceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 2014;42:D92-97.
    • (2014) Nucleic Acids Res , vol.42 , pp. D92-D97
    • Li, J.1    Liu, S.2    Zhou, H.3
  • 70
    • 84902279606 scopus 로고    scopus 로고
    • lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome
    • Chan W, Huang H, Chang J. lncRNAMap: a map of putative regulatory functions in the long non-coding transcriptome. Comput Biol Chem 2014;50:41-9.
    • (2014) Comput Biol Chem , vol.50 , pp. 41-49
    • Chan, W.1    Huang, H.2    Chang, J.3
  • 71
    • 84876523096 scopus 로고    scopus 로고
    • DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs
    • Paraskevopoulou M, Georgakilas G, Kostoulas N, et al. DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res 2013;41:D239-45.
    • (2013) Nucleic Acids Res , vol.41 , pp. D239-D245
    • Paraskevopoulou, M.1    Georgakilas, G.2    Kostoulas, N.3
  • 72
    • 84876566914 scopus 로고    scopus 로고
    • ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data
    • Yang J, Li J, Zhou H, et al. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res 2013;41:D177-87.
    • (2013) Nucleic Acids Res , vol.41 , pp. D177-D187
    • Yang, J.1    Li, J.2    Zhou, H.3
  • 73
    • 84939498768 scopus 로고    scopus 로고
    • Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA
    • Chen X. Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. Sci Rep 2015;5:13186 EP.
    • (2015) Sci Rep , vol.5
    • Chen, X.1
  • 74
    • 84865138690 scopus 로고    scopus 로고
    • miRcode: a map of putative microRNA target sites in the long non-coding transcriptome
    • Jeggari A, Marks D, Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics 2012;28:2062-3.
    • (2012) Bioinformatics , vol.28 , pp. 2062-2063
    • Jeggari, A.1    Marks, D.2    Larsson, E.3
  • 76
    • 84885912472 scopus 로고    scopus 로고
    • lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
    • Bhartiya D, Pal K, Ghosh S, et al. lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Oxford 2013;2013:bat034.
    • (2013) Oxford , vol.2013
    • Bhartiya, D.1    Pal, K.2    Ghosh, S.3
  • 77
    • 84868683235 scopus 로고    scopus 로고
    • SmD3 regulates intronic noncoding RNA biogenesis
    • Scruggs BS, Michel CI, Ory DS, et al. SmD3 regulates intronic noncoding RNA biogenesis. Mol Cell Biol 2012;32:4092-103.
    • (2012) Mol Cell Biol , vol.32 , pp. 4092-4103
    • Scruggs, B.S.1    Michel, C.I.2    Ory, D.S.3
  • 78
    • 38949145743 scopus 로고    scopus 로고
    • Serum proteomics and biomarkers in hepatocellular carcinoma and chronic liver disease
    • Zinkin N, Grall F, Bhaskar K, et al. Serum proteomics and biomarkers in hepatocellular carcinoma and chronic liver disease, Clin Cancer Res 2008.
    • (2008) Clin Cancer Res
    • Zinkin, N.1    Grall, F.2    Bhaskar, K.3
  • 79
    • 84863425849 scopus 로고    scopus 로고
    • Small RNAs have a large impact: Circulating microRNAs as biomarkers for human diseases
    • Weiland M, Gao X, Zhou L, et al. Small RNAs have a large impact: Circulating microRNAs as biomarkers for human diseases. RNA Biol 2012;9:850-9.
    • (2012) RNA Biol , vol.9 , pp. 850-859
    • Weiland, M.1    Gao, X.2    Zhou, L.3
  • 80
    • 84904748043 scopus 로고    scopus 로고
    • Analysing the relationship between lncRNA and protein-coding gene and the role of lncRNA as ceRNA in pulmonary fibrosis
    • Song X, Cao G, Jing L, et al. Analysing the relationship between lncRNA and protein-coding gene and the role of lncRNA as ceRNA in pulmonary fibrosis. J Cell Mol Med 2014;18:991-1003.
    • (2014) J Cell Mol Med , vol.18 , pp. 991-1003
    • Song, X.1    Cao, G.2    Jing, L.3
  • 81
    • 85044694480 scopus 로고    scopus 로고
    • RNAcentral: an international database of ncRNA sequences
    • Consortium R. RNAcentral: an international database of ncRNA sequences. Nucleic Acids Res 2014;43:D123-9.
    • (2014) Nucleic Acids Res , vol.43 , pp. D123-D129
    • Consortium, R.1
  • 82
    • 84943156256 scopus 로고    scopus 로고
    • Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data
    • Zhao Z, Bai J, Wu A, et al. Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data. Oxford 2015;2015:1-7.
    • (2015) Oxford , vol.2015 , pp. 1-7
    • Zhao, Z.1    Bai, J.2    Wu, A.3
  • 83
    • 84965186421 scopus 로고    scopus 로고
    • LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
    • Jiang Q, Ma R, Wang J, et al. LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. BMC Genomics 2015;16:S2.
    • (2015) BMC Genomics , vol.16 , pp. S2
    • Jiang, Q.1    Ma, R.2    Wang, J.3
  • 84
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: the reference human genome annotation for The ENCODE project
    • Harrow J, Frankish A, Gonzalez J, et al. GENCODE: the reference human genome annotation for The ENCODE project. Genome Res 2012;22:1760-74.
    • (2012) Genome Res , vol.22 , pp. 1760-1774
    • Harrow, J.1    Frankish, A.2    Gonzalez, J.3
  • 85
    • 84882643385 scopus 로고    scopus 로고
    • Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis
    • Liu K, Yan Z, Li Y, et al. Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis. Bioinformatics 2013;29:2221-2.
    • (2013) Bioinformatics , vol.29 , pp. 2221-2222
    • Liu, K.1    Yan, Z.2    Li, Y.3
  • 86
    • 79956010263 scopus 로고    scopus 로고
    • Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene coexpression network
    • Liao Q, Liu C, Yuan X, et al. Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene coexpression network. Nucleic Acids Res 2011;39:3864-78.
    • (2011) Nucleic Acids Res , vol.39 , pp. 3864-3878
    • Liao, Q.1    Liu, C.2    Yuan, X.3
  • 87
    • 79959949911 scopus 로고    scopus 로고
    • ncFANs: a web server for functional annotation of long non-coding RNAs
    • Liao Q, Xiao H, Bu D, et al. ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res 2011;39:W118-24.
    • (2011) Nucleic Acids Res , vol.39 , pp. W118-W124
    • Liao, Q.1    Xiao, H.2    Bu, D.3
  • 88
    • 84946065958 scopus 로고    scopus 로고
    • lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse
    • Gong G, Liu W, Zhang J, et al. lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res 2015;43:D181-6.
    • (2015) Nucleic Acids Res , vol.43 , pp. D181-D186
    • Gong, G.1    Liu, W.2    Zhang, J.3
  • 89
    • 84876125829 scopus 로고    scopus 로고
    • LncRNADisease: a database for long-non-coding RNA-associated diseases
    • Chen G, Wang Z, Wang D, et al. LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res 2013;41:D983-6.
    • (2013) Nucleic Acids Res , vol.41 , pp. D983-D986
    • Chen, G.1    Wang, Z.2    Wang, D.3
  • 90
    • 79959949911 scopus 로고    scopus 로고
    • ncFANs: a web server for functional annotation of long non-coding RNAs
    • Liao Q, Xiao H, Bu D, et al. ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res 2011;39:W118-24.
    • (2011) Nucleic Acids Res , vol.39 , pp. W118-W124
    • Liao, Q.1    Xiao, H.2    Bu, D.3
  • 91
    • 84907032373 scopus 로고    scopus 로고
    • lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs
    • Park C, Yu N, Choi I, et al. lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs. Bioinformatics 2014;30:2480-5.
    • (2014) Bioinformatics , vol.30 , pp. 2480-2485
    • Park, C.1    Yu, N.2    Choi, I.3
  • 92
    • 84884837017 scopus 로고    scopus 로고
    • Computational prediction of associations between long non-coding RNAs and proteins
    • Lu Q, Ren S, Lu M, et al. Computational prediction of associations between long non-coding RNAs and proteins. BMC Genomics 2013;24:651.
    • (2013) BMC Genomics , vol.24 , pp. 651
    • Lu, Q.1    Ren, S.2    Lu, M.3
  • 93
    • 84876523096 scopus 로고    scopus 로고
    • DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs
    • Paraskevopoulou MD, Georgakilas G, Kostoulas N, et al. DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res 2013;41:D239-45.
    • (2013) Nucleic Acids Res , vol.41 , pp. D239-D245
    • Paraskevopoulou, M.D.1    Georgakilas, G.2    Kostoulas, N.3
  • 94
    • 79955581917 scopus 로고    scopus 로고
    • MicroRNAs and epigenetics
    • Sato F, Tsuchiya S, Meltzer SJ, et al. MicroRNAs and epigenetics. FEBS J 2011;278:1598-609.
    • (2011) FEBS J , vol.278 , pp. 1598-1609
    • Sato, F.1    Tsuchiya, S.2    Meltzer, S.J.3
  • 95
    • 84865344002 scopus 로고    scopus 로고
    • The plant Mediator and its role in noncoding RNA production
    • Kim YJ, Chen X. The plant Mediator and its role in noncoding RNA production. Front Biol 2011;6:125-32.
    • (2011) Front Biol , vol.6 , pp. 125-132
    • Kim, Y.J.1    Chen, X.2
  • 96
    • 84897833980 scopus 로고    scopus 로고
    • TF2LncRNA: identifying common transcription factors for a list of lncRNA genes from ChIP-Seq data
    • Jiang Q, Wang J, Wang Y, et al. TF2LncRNA: identifying common transcription factors for a list of lncRNA genes from ChIP-Seq data. Biomed Res Int 2014;2014:317642.
    • (2014) Biomed Res Int , vol.2014
    • Jiang, Q.1    Wang, J.2    Wang, Y.3
  • 97
    • 84942909779 scopus 로고    scopus 로고
    • TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer
    • Li J, Han J, Roebuck P, et al. TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer. Cancer Res 2015;75:3728-37.
    • (2015) Cancer Res , vol.75 , pp. 3728-3737
    • Li, J.1    Han, J.2    Roebuck, P.3
  • 98
    • 84928999780 scopus 로고    scopus 로고
    • LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis
    • He S, Zhang H, Liu H, et al. LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis. Bioinformatics 2015;31:178-86.
    • (2015) Bioinformatics , vol.31 , pp. 178-186
    • He, S.1    Zhang, H.2    Liu, H.3
  • 99
    • 84924063355 scopus 로고    scopus 로고
    • The landscape of long noncoding RNAs in the human transcriptome
    • Iyer M, Niknafs Y, Malik R, et al. The landscape of long noncoding RNAs in the human transcriptome. Nature Genetics 2015;47:199-208.
    • (2015) Nature Genetics , vol.47 , pp. 199-208
    • Iyer, M.1    Niknafs, Y.2    Malik, R.3
  • 101
    • 33644893631 scopus 로고    scopus 로고
    • Coarse-grained protein-lipid model with application to lipoprotein particles
    • Shih AY, Arkipov A, Freddolino PL, et al. Coarse-grained protein-lipid model with application to lipoprotein particles. J Phys Chem 2006;110:3674-84.
    • (2006) J Phys Chem , vol.110 , pp. 3674-3684
    • Shih, A.Y.1    Arkipov, A.2    Freddolino, P.L.3


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