메뉴 건너뛰기




Volumn 8, Issue 8, 2013, Pages

Visualized Computational Predictions of Transcriptional Effects by Intronic Endogenous Retroviruses

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFICIAL NEURAL NETWORK; DNA POLYMORPHISM; EARLY TRANSPOSON; FEASIBILITY STUDY; GENE INSERTION; GENE MUTATION; GENETIC TRANSCRIPTION; INTRACISTERNAL A TYPE PARTICLE; INTRON; MACHINE LEARNING; MATHEMATICAL ANALYSIS; MUSD ELEMENT; NONHUMAN; PREDICTION; RELIABILITY; RETROVIRUS; TRANSPOSON;

EID: 84881185055     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0071971     Document Type: Article
Times cited : (6)

References (31)
  • 1
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • doi:10.1038/35057062
    • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921 doi:10.1038/35057062.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.S.1    Linton, L.M.2    Birren, B.3    Nusbaum, C.4    Zody, M.C.5
  • 2
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • doi:10.1038/nature01262
    • Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562 doi:10.1038/nature01262.
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1    Lindblad-Toh, K.2    Birney, E.3    Rogers, J.4    Abril, J.F.5
  • 3
    • 33645757337 scopus 로고    scopus 로고
    • Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line
    • doi:10.1371/journal.pgen.0020002
    • Maksakova IA, Romanish MT, Gagnier L, Dunn CA, van de Lagemaat LN, et al. (2006) Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PLoS genetics 2: e2 doi:10.1371/journal.pgen.0020002.
    • (2006) PLoS Genetics , vol.2
    • Maksakova, I.A.1    Romanish, M.T.2    Gagnier, L.3    Dunn, C.A.4    van de Lagemaat, L.N.5
  • 4
    • 40149098109 scopus 로고    scopus 로고
    • Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements
    • doi:10.1371/journal.pgen.1000007
    • Zhang Y, Maksakova IA, Gagnier L, van de Lagemaat LN, Mager DL, (2008) Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PLoS genetics 4: e1000007 doi:10.1371/journal.pgen.1000007.
    • (2008) PLoS Genetics , vol.4
    • Zhang, Y.1    Maksakova, I.A.2    Gagnier, L.3    van de Lagemaat, L.N.4    Mager, D.L.5
  • 5
    • 84862203271 scopus 로고    scopus 로고
    • The genomic landscape shaped by selection on transposable elements across 18 mouse strains
    • doi:10.1186/gb-2012-13-6-r45
    • Nellaker C, Keane TM, Yalcin B, Wong K, Agam A, et al. (2012) The genomic landscape shaped by selection on transposable elements across 18 mouse strains. Genome biology 13: R45 doi:10.1186/gb-2012-13-6-r45.
    • (2012) Genome Biology , vol.13
    • Nellaker, C.1    Keane, T.M.2    Yalcin, B.3    Wong, K.4    Agam, A.5
  • 6
    • 84858439844 scopus 로고    scopus 로고
    • Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
    • doi:10.1101/gr.130740.111
    • Li J, Akagi K, Hu Y, Trivett AL, Hlynialuk CJ, et al. (2012) Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance. Genome research doi:10.1101/gr.130740.111.
    • (2012) Genome Research
    • Li, J.1    Akagi, K.2    Hu, Y.3    Trivett, A.L.4    Hlynialuk, C.J.5
  • 7
    • 5744230326 scopus 로고    scopus 로고
    • Disruption of muscle membrane and phenotype divergence in two novel mouse models of dysferlin deficiency
    • doi:10.1093/hmg/ddh212
    • Ho M, Post CM, Donahue LR, Lidov HGW, Bronson RT, et al. (2004) Disruption of muscle membrane and phenotype divergence in two novel mouse models of dysferlin deficiency. Hum Mol Genet 13: 1999-2010 doi:10.1093/hmg/ddh212.
    • (2004) Hum Mol Genet , vol.13 , pp. 1999-2010
    • Ho, M.1    Post, C.M.2    Donahue, L.R.3    Lidov, H.G.W.4    Bronson, R.T.5
  • 8
    • 7444264729 scopus 로고    scopus 로고
    • Complex patterns of transcription at the insertion site of a retrotransposon in the mouse
    • doi:10.1093/nar/gkh914
    • Druker R, Bruxner TJ, Lehrbach NJ, Whitelaw E, (2004) Complex patterns of transcription at the insertion site of a retrotransposon in the mouse. Nucleic acids research 32: 5800-5808 doi:10.1093/nar/gkh914.
    • (2004) Nucleic Acids Research , vol.32 , pp. 5800-5808
    • Druker, R.1    Bruxner, T.J.2    Lehrbach, N.J.3    Whitelaw, E.4
  • 9
    • 0032784908 scopus 로고    scopus 로고
    • Interspersed repeats and other mementos of transposable elements in mammalian genomes
    • Smit AF, (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9: 657-663.
    • (1999) Curr Opin Genet Dev , vol.9 , pp. 657-663
    • Smit, A.F.1
  • 10
    • 0036798062 scopus 로고    scopus 로고
    • Retroelement distributions in the human genome: variations associated with age and proximity to genes
    • doi:10.1101/gr.388902
    • Medstrand P, van de Lagemaat LN, Mager DL, (2002) Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome research 12: 1483-1495 doi:10.1101/gr.388902.
    • (2002) Genome Research , vol.12 , pp. 1483-1495
    • Medstrand, P.1    van de Lagemaat, L.N.2    Mager, D.L.3
  • 11
    • 33750460928 scopus 로고    scopus 로고
    • Multiple effects govern endogenous retrovirus survival patterns in human gene introns
    • doi:10.1186/gb-2006-7-9-r86
    • van de Lagemaat LN, Medstrand P, Mager DL, (2006) Multiple effects govern endogenous retrovirus survival patterns in human gene introns. Genome biology 7: R86 doi:10.1186/gb-2006-7-9-r86.
    • (2006) Genome Biology , vol.7
    • van de Lagemaat, L.N.1    Medstrand, P.2    Mager, D.L.3
  • 12
    • 28244471042 scopus 로고    scopus 로고
    • Transposable element orientation bias in the Drosophila melanogaster genome
    • doi:10.1007/s00239-004-0243-0
    • Cutter AD, Good JM, Pappas CT, Saunders MA, Starrett DM, et al. (2005) Transposable element orientation bias in the Drosophila melanogaster genome. J Mol Evol 61: 733-741 doi:10.1007/s00239-004-0243-0.
    • (2005) J Mol Evol , vol.61 , pp. 733-741
    • Cutter, A.D.1    Good, J.M.2    Pappas, C.T.3    Saunders, M.A.4    Starrett, D.M.5
  • 13
    • 79958117110 scopus 로고    scopus 로고
    • Distributions of transposable elements reveal hazardous zones in Mammalian introns
    • doi:10.1371/journal.pcbi.1002046
    • Zhang Y, Romanish MT, Mager DL, (2011) Distributions of transposable elements reveal hazardous zones in Mammalian introns. PLoS Comput Biol 7: e1002046 doi:10.1371/journal.pcbi.1002046.
    • (2011) PLoS Comput Biol , vol.7
    • Zhang, Y.1    Romanish, M.T.2    Mager, D.L.3
  • 14
    • 0042836785 scopus 로고    scopus 로고
    • Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22
    • doi:10.1093/molbev/msg153, C BR
    • Grover D, Majumder PP, C BR, Brahmachari SK, Mukerji M, (2003) Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22. Mol Biol Evol 20: 1420-1424 doi:10.1093/molbev/msg153.
    • (2003) Mol Biol Evol , vol.20 , pp. 1420-1424
    • Grover, D.1    Majumder, P.P.2    Brahmachari, S.K.3    Mukerji, M.4
  • 15
    • 77957579304 scopus 로고    scopus 로고
    • Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species
    • doi:10.1007/s00239-010-9376-5
    • Mortada H, Vieira C, Lerat E, (2010) Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species. J Mol Evol 71: 180-191 doi:10.1007/s00239-010-9376-5.
    • (2010) J Mol Evol , vol.71 , pp. 180-191
    • Mortada, H.1    Vieira, C.2    Lerat, E.3
  • 16
    • 34249752804 scopus 로고    scopus 로고
    • Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns
    • doi:10.1186/gb-2006-7-12-r120
    • Sironi M, Menozzi G, Comi GP, Cereda M, Cagliani R, et al. (2006) Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome biology 7: R120 doi:10.1186/gb-2006-7-12-r120.
    • (2006) Genome Biology , vol.7
    • Sironi, M.1    Menozzi, G.2    Comi, G.P.3    Cereda, M.4    Cagliani, R.5
  • 17
    • 84855858788 scopus 로고    scopus 로고
    • Gene properties and chromatin state influence the accumulation of transposable elements in genes
    • doi:10.1371/journal.pone.0030158
    • Zhang Y, Mager DL, (2012) Gene properties and chromatin state influence the accumulation of transposable elements in genes. PloS one 7: e30158 doi:10.1371/journal.pone.0030158.
    • (2012) PloS One , vol.7
    • Zhang, Y.1    Mager, D.L.2
  • 18
    • 0030297904 scopus 로고    scopus 로고
    • Advantages and disadvantages of using artificial neural networks versus logistic regression for predicting medical outcomes
    • Tu JV, (1996) Advantages and disadvantages of using artificial neural networks versus logistic regression for predicting medical outcomes. J Clin Epidemiol 49: 1225-1231.
    • (1996) J Clin Epidemiol , vol.49 , pp. 1225-1231
    • Tu, J.V.1
  • 19
    • 55549096355 scopus 로고    scopus 로고
    • Murine endogenous retroviruses
    • doi:10.1007/s00018-008-8497-0
    • Stocking C, Kozak CA, (2008) Murine endogenous retroviruses. Cell Mol Life Sci 65: 3383-3398 doi:10.1007/s00018-008-8497-0.
    • (2008) Cell Mol Life Sci , vol.65 , pp. 3383-3398
    • Stocking, C.1    Kozak, C.A.2
  • 20
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • doi:10.1089/1066527041410418
    • Yeo G, Burge CB, (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 11: 377-394 doi:10.1089/1066527041410418.
    • (2004) J Comput Biol , vol.11 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2
  • 22
    • 84875377539 scopus 로고    scopus 로고
    • Retroelements in human disease
    • doi:10.1016/j.gene.2013.01.008
    • Kaer K, Speek M, (2013) Retroelements in human disease. Gene doi:10.1016/j.gene.2013.01.008.
    • (2013) Gene
    • Kaer, K.1    Speek, M.2
  • 23
    • 84867050577 scopus 로고    scopus 로고
    • Transposable elements: an abundant and natural source of regulatory sequences for host genes
    • doi:10.1146/annurev-genet-110711-155621
    • Rebollo R, Romanish MT, Mager DL, (2012) Transposable elements: an abundant and natural source of regulatory sequences for host genes. Annu Rev Genet 46: 21-42 doi:10.1146/annurev-genet-110711-155621.
    • (2012) Annu Rev Genet , vol.46 , pp. 21-42
    • Rebollo, R.1    Romanish, M.T.2    Mager, D.L.3
  • 24
    • 77955160719 scopus 로고    scopus 로고
    • High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
    • doi:10.1101/gr.106419.110
    • Ewing AD, Kazazian HHJ, (2010) High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome research 20: 1262-1270 doi:10.1101/gr.106419.110.
    • (2010) Genome Research , vol.20 , pp. 1262-1270
    • Ewing, A.D.1    Kazazian, H.H.J.2
  • 25
    • 77953892366 scopus 로고    scopus 로고
    • Mobile interspersed repeats are major structural variants in the human genome
    • doi:10.1016/j.cell.2010.05.026
    • Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, et al. (2010) Mobile interspersed repeats are major structural variants in the human genome. Cell 141: 1171-1182 doi:10.1016/j.cell.2010.05.026.
    • (2010) Cell , vol.141 , pp. 1171-1182
    • Huang, C.R.1    Schneider, A.M.2    Lu, Y.3    Niranjan, T.4    Shen, P.5
  • 26
    • 77953880842 scopus 로고    scopus 로고
    • LINE-1 retrotransposition activity in human genomes
    • doi:10.1016/j.cell.2010.05.021
    • Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, et al. (2010) LINE-1 retrotransposition activity in human genomes. Cell 141: 1159-1170 doi:10.1016/j.cell.2010.05.021.
    • (2010) Cell , vol.141 , pp. 1159-1170
    • Beck, C.R.1    Collier, P.2    Macfarlane, C.3    Malig, M.4    Kidd, J.M.5
  • 27
    • 77953889472 scopus 로고    scopus 로고
    • Natural mutagenesis of human genomes by endogenous retrotransposons
    • doi:10.1016/j.cell.2010.05.020
    • Iskow RC, McCabe MT, Mills RE, Torene S, Pittard WS, et al. (2010) Natural mutagenesis of human genomes by endogenous retrotransposons. Cell 141: 1253-1261 doi:10.1016/j.cell.2010.05.020.
    • (2010) Cell , vol.141 , pp. 1253-1261
    • Iskow, R.C.1    McCabe, M.T.2    Mills, R.E.3    Torene, S.4    Pittard, W.S.5
  • 28
    • 84865285978 scopus 로고    scopus 로고
    • Landscape of somatic retrotransposition in human cancers
    • doi:10.1126/science.1222077
    • Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, et al. (2012) Landscape of somatic retrotransposition in human cancers. Science 337: 967-971 doi:10.1126/science.1222077.
    • (2012) Science , vol.337 , pp. 967-971
    • Lee, E.1    Iskow, R.2    Yang, L.3    Gokcumen, O.4    Haseley, P.5
  • 29
    • 81855178276 scopus 로고    scopus 로고
    • Somatic retrotransposition alters the genetic landscape of the human brain
    • doi:10.1038/nature10531
    • Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, et al. (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479: 534-537 doi:10.1038/nature10531.
    • (2011) Nature , vol.479 , pp. 534-537
    • Baillie, J.K.1    Barnett, M.W.2    Upton, K.R.3    Gerhardt, D.J.4    Richmond, T.A.5
  • 30
    • 84868032982 scopus 로고    scopus 로고
    • Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain
    • doi:10.1016/j.cell.2012.09.035
    • Evrony GD, Cai X, Lee E, Hills LB, Elhosary PC, et al. (2012) Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 151: 483-496 doi:10.1016/j.cell.2012.09.035.
    • (2012) Cell , vol.151 , pp. 483-496
    • Evrony, G.D.1    Cai, X.2    Lee, E.3    Hills, L.B.4    Elhosary, P.C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.