메뉴 건너뛰기




Volumn 14, Issue SUPPL7, 2013, Pages

Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR DIFFERENTIATION; CENTRAL NERVOUS SYSTEMS; COMPUTATIONAL EVALUATION; FUNCTIONAL ANNOTATION; GENOMIC ARCHITECTURE; PROTEIN-CODING GENES; REGULATION OF TRANSCRIPTION; SEQUENCE CONSERVATION;

EID: 84887180777     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S7-S14     Document Type: Article
Times cited : (19)

References (73)
  • 1
    • 9144252038 scopus 로고    scopus 로고
    • Complete sequencing and characterization of 21,243 full-length human cDNAs
    • 10.1038/ng1285, 14702039
    • Ota T, Suzuki Y, Nishikawa T, et al. Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet 2004, 36:40-45. 10.1038/ng1285, 14702039.
    • (2004) Nat Genet , vol.36 , pp. 40-45
    • Ota, T.1    Suzuki, Y.2    Nishikawa, T.3
  • 2
    • 0142104045 scopus 로고    scopus 로고
    • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    • 10.1038/nature01266, 12466851
    • Okazaki Y, Furuno M, Kasukawa T, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002, 420:563-573. 10.1038/nature01266, 12466851.
    • (2002) Nature , vol.420 , pp. 563-573
    • Okazaki, Y.1    Furuno, M.2    Kasukawa, T.3
  • 3
    • 24644519490 scopus 로고    scopus 로고
    • The transcriptional landscape of the mammalian genome
    • Carninci P, Kasukawa T, Katayama S, et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559-1563.
    • (2005) Science , vol.309 , pp. 1559-1563
    • Carninci, P.1    Kasukawa, T.2    Katayama, S.3
  • 4
    • 0026456701 scopus 로고
    • The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus
    • 10.1016/0092-8674(92)90520-M, 1423611
    • Brown CJ, Hendrich BD, Rupert JL, Lafrenière RG, Xing Y, Lawrence J, Willard HF. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992, 71:527-542. 10.1016/0092-8674(92)90520-M, 1423611.
    • (1992) Cell , vol.71 , pp. 527-542
    • Brown, C.J.1    Hendrich, B.D.2    Rupert, J.L.3    Lafrenière, R.G.4    Xing, Y.5    Lawrence, J.6    Willard, H.F.7
  • 5
    • 0037382133 scopus 로고    scopus 로고
    • Identification of new Xlsirt family members in the Xenopus laevis oocyte
    • 10.1016/S0925-4773(02)00459-8, 12676327
    • Zearfoss NR, Chan AP, Kloc M, Allen LH, Etkin LD. Identification of new Xlsirt family members in the Xenopus laevis oocyte. Mech Dev 2003, 120:503-509. 10.1016/S0925-4773(02)00459-8, 12676327.
    • (2003) Mech Dev , vol.120 , pp. 503-509
    • Zearfoss, N.R.1    Chan, A.P.2    Kloc, M.3    Allen, L.H.4    Etkin, L.D.5
  • 8
    • 77951638287 scopus 로고    scopus 로고
    • Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor
    • 10.1126/scisignal.2000568, 2819218, 20124551
    • Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP. Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal 2010, 3:ra8. 10.1126/scisignal.2000568, 2819218, 20124551.
    • (2010) Sci Signal , vol.3
    • Kino, T.1    Hurt, D.E.2    Ichijo, T.3    Nader, N.4    Chrousos, G.P.5
  • 9
    • 33847185603 scopus 로고    scopus 로고
    • A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains
    • 10.1186/1471-2164-8-39, 1800850, 17270048
    • Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 2007, 8:39. 10.1186/1471-2164-8-39, 1800850, 17270048.
    • (2007) BMC Genomics , vol.8 , pp. 39
    • Hutchinson, J.N.1    Ensminger, A.W.2    Clemson, C.M.3    Lynch, C.R.4    Lawrence, J.B.5    Chess, A.6
  • 11
    • 67649160600 scopus 로고    scopus 로고
    • Genome-wide identification of long noncoding RNAs in CD8+ T cells
    • 10.4049/jimmunol.0900603, 19494298
    • Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS. Genome-wide identification of long noncoding RNAs in CD8+ T cells. J Immunol 2009, 182:7738-7748. 10.4049/jimmunol.0900603, 19494298.
    • (2009) J Immunol , vol.182 , pp. 7738-7748
    • Pang, K.C.1    Dinger, M.E.2    Mercer, T.R.3    Malquori, L.4    Grimmond, S.M.5    Chen, W.6    Mattick, J.S.7
  • 12
    • 77952952164 scopus 로고    scopus 로고
    • Identification of long stress-induced non-coding transcripts that have altered expression in cancer
    • 10.1016/j.ygeno.2010.02.009, 20214974
    • Silva JM, Perez DS, Pritchett JR, Halling ML, Tang H, Smith DI. Identification of long stress-induced non-coding transcripts that have altered expression in cancer. Genomics 2010, 95:355-362. 10.1016/j.ygeno.2010.02.009, 20214974.
    • (2010) Genomics , vol.95 , pp. 355-362
    • Silva, J.M.1    Perez, D.S.2    Pritchett, J.R.3    Halling, M.L.4    Tang, H.5    Smith, D.I.6
  • 14
    • 76649122999 scopus 로고    scopus 로고
    • Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation
    • 10.1186/1471-2202-11-14, 2829031, 20137068
    • Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS, Mehler MF. Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 2010, 11:14. 10.1186/1471-2202-11-14, 2829031, 20137068.
    • (2010) BMC Neurosci , vol.11 , pp. 14
    • Mercer, T.R.1    Qureshi, I.A.2    Gokhan, S.3    Dinger, M.E.4    Li, G.5    Mattick, J.S.6    Mehler, M.F.7
  • 15
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • 10.1038/nrg2484, 2949280, 19015660
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63. 10.1038/nrg2484, 2949280, 19015660.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 16
    • 80052536392 scopus 로고    scopus 로고
    • RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders
    • 10.1371/journal.pone.0023356, 3168439, 21915259
    • Lin M, Pedrosa E, Shah A, Hrabovsky A, Maqbool S, Zheng D, Lachman HM. RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. PLoS ONE 2011, 6:e23356. 10.1371/journal.pone.0023356, 3168439, 21915259.
    • (2011) PLoS ONE , vol.6
    • Lin, M.1    Pedrosa, E.2    Shah, A.3    Hrabovsky, A.4    Maqbool, S.5    Zheng, D.6    Lachman, H.M.7
  • 18
    • 84455206362 scopus 로고    scopus 로고
    • Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution
    • 10.1016/j.cell.2011.11.055, 3376356, 22196729
    • Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP. Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution. Cell 2011, 147:1537-1550. 10.1016/j.cell.2011.11.055, 3376356, 22196729.
    • (2011) Cell , vol.147 , pp. 1537-1550
    • Ulitsky, I.1    Shkumatava, A.2    Jan, C.H.3    Sive, H.4    Bartel, D.P.5
  • 21
    • 77956411754 scopus 로고    scopus 로고
    • Mining mammalian transcript data for functional long non-coding RNAs
    • 10.1371/journal.pone.0010316, 2859052, 20428234
    • Khachane AN, Harrison PM. Mining mammalian transcript data for functional long non-coding RNAs. PLoS ONE 2010, 5:e10316. 10.1371/journal.pone.0010316, 2859052, 20428234.
    • (2010) PLoS ONE , vol.5
    • Khachane, A.N.1    Harrison, P.M.2
  • 22
    • 77955110979 scopus 로고    scopus 로고
    • Genome-wide computational identification and manual annotation of human long noncoding RNA genes
    • 10.1261/rna.1951310, 2905748, 20587619
    • Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA 2010, 16:1478-1487. 10.1261/rna.1951310, 2905748, 20587619.
    • (2010) RNA , vol.16 , pp. 1478-1487
    • Jia, H.1    Osak, M.2    Bogu, G.K.3    Stanton, L.W.4    Johnson, R.5    Lipovich, L.6
  • 23
    • 69349102207 scopus 로고    scopus 로고
    • Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis
    • 10.1186/1471-2105-10-239, 2731755, 19653905
    • Arrial R, Togawa R, Brigido M. Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. BMC Bioinformatics 2009, 10:239. 10.1186/1471-2105-10-239, 2731755, 19653905.
    • (2009) BMC Bioinformatics , vol.10 , pp. 239
    • Arrial, R.1    Togawa, R.2    Brigido, M.3
  • 24
    • 34547582418 scopus 로고    scopus 로고
    • CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
    • 10.1093/nar/gkm391, 1933232, 17631615
    • Kong L, Zhang Y, Ye Z-Q, Liu X-Q, Zhao S-Q, Wei L, Gao G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 2007, 35:W345-349. 10.1093/nar/gkm391, 1933232, 17631615.
    • (2007) Nucleic Acids Res , vol.35
    • Kong, L.1    Zhang, Y.2    Ye, Z.-Q.3    Liu, X.-Q.4    Zhao, S.-Q.5    Wei, L.6    Gao, G.7
  • 25
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • 10.1101/gad.17446611, 3579889, 23451280
    • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & Development 2011, 25:1915-1927. 10.1101/gad.17446611, 3579889, 23451280.
    • (2011) Genes & Development , vol.25 , pp. 1915-1927
    • Cabili, M.N.1    Trapnell, C.2    Goff, L.3    Koziol, M.4    Tazon-Vega, B.5    Regev, A.6    Rinn, J.L.7
  • 26
    • 77954399763 scopus 로고    scopus 로고
    • Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes
    • 10.1186/gb-2010-11-7-r72, 2926783, 20624288
    • Chodroff RA, Goodstadt L, Sirey TM, Oliver PL, Davies KE, Green ED, Molnár Z, Ponting CP. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol 2010, 11:R72. 10.1186/gb-2010-11-7-r72, 2926783, 20624288.
    • (2010) Genome Biol , vol.11
    • Chodroff, R.A.1    Goodstadt, L.2    Sirey, T.M.3    Oliver, P.L.4    Davies, K.E.5    Green, E.D.6    Molnár, Z.7    Ponting, C.P.8
  • 28
    • 33745125901 scopus 로고    scopus 로고
    • The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene
    • 10.1126/science.1126316, 16778056
    • Duret L, Chureau C, Samain S, Weissenbach J, Avner P. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science 2006, 312:1653-1655. 10.1126/science.1126316, 16778056.
    • (2006) Science , vol.312 , pp. 1653-1655
    • Duret, L.1    Chureau, C.2    Samain, S.3    Weissenbach, J.4    Avner, P.5
  • 30
    • 70350118664 scopus 로고    scopus 로고
    • Complex architecture and regulated expression of the Sox2ot locus during vertebrate development
    • 10.1261/rna.1705309, 2764477, 19767420
    • Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC, Mattick JS. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA 2009, 15:2013-2027. 10.1261/rna.1705309, 2764477, 19767420.
    • (2009) RNA , vol.15 , pp. 2013-2027
    • Amaral, P.P.1    Neyt, C.2    Wilkins, S.J.3    Askarian-Amiri, M.E.4    Sunkin, S.M.5    Perkins, A.C.6    Mattick, J.S.7
  • 31
    • 70149123708 scopus 로고    scopus 로고
    • Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
    • 10.1371/journal.pgen.1000617, 2722021, 19696892
    • Ponjavic J, Oliver PL, Lunter G, Ponting CP. Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet 2009, 5:e1000617. 10.1371/journal.pgen.1000617, 2722021, 19696892.
    • (2009) PLoS Genet , vol.5
    • Ponjavic, J.1    Oliver, P.L.2    Lunter, G.3    Ponting, C.P.4
  • 32
    • 80053523254 scopus 로고    scopus 로고
    • The evolution of RNAs with multiple functions
    • 10.1016/j.biochi.2011.07.018, 21802485
    • Dinger ME, Gascoigne DK, Mattick JS. The evolution of RNAs with multiple functions. Biochimie 2011, 93:2013-2018. 10.1016/j.biochi.2011.07.018, 21802485.
    • (2011) Biochimie , vol.93 , pp. 2013-2018
    • Dinger, M.E.1    Gascoigne, D.K.2    Mattick, J.S.3
  • 33
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • 10.1016/j.cell.2011.10.002, 3225288, 22056041
    • Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 2011, 147:789-802. 10.1016/j.cell.2011.10.002, 3225288, 22056041.
    • (2011) Cell , vol.147 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 35
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • 10.1101/gr.097857.109, 2798823, 19858363
    • Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 2010, 20:110-121. 10.1101/gr.097857.109, 2798823, 19858363.
    • (2010) Genome Res , vol.20 , pp. 110-121
    • Pollard, K.S.1    Hubisz, M.J.2    Rosenbloom, K.R.3    Siepel, A.4
  • 36
    • 84887207865 scopus 로고    scopus 로고
    • http://www.ensembl.org/info/docs/genebuild/ncrna.html
  • 38
    • 26944454497 scopus 로고    scopus 로고
    • ROC graphs: Notes and practical considerations for researchers
    • Fawcett T. ROC graphs: Notes and practical considerations for researchers. Machine Learning 2004, 31:1-38.
    • (2004) Machine Learning , vol.31 , pp. 1-38
    • Fawcett, T.1
  • 39
    • 84869881863 scopus 로고    scopus 로고
    • Transposable elements reveal a stem cell specific class of long noncoding RNAs
    • 10.1186/gb-2012-13-11-r107, 3580499, 23181609
    • Kelley DR, Rinn JL. Transposable elements reveal a stem cell specific class of long noncoding RNAs. Genome Biology 2012, 13:R107. 10.1186/gb-2012-13-11-r107, 3580499, 23181609.
    • (2012) Genome Biology , vol.13
    • Kelley, D.R.1    Rinn, J.L.2
  • 41
    • 14044272835 scopus 로고    scopus 로고
    • Fast and reliable prediction of noncoding RNAs
    • 10.1073/pnas.0409169102, 548974, 15665081
    • Washietl S, Hofacker IL, Stadler PF. Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci USA 2005, 102:2454-2459. 10.1073/pnas.0409169102, 548974, 15665081.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 2454-2459
    • Washietl, S.1    Hofacker, I.L.2    Stadler, P.F.3
  • 42
    • 36049029123 scopus 로고    scopus 로고
    • Detection of RNA structures in porcine EST data and related mammals
    • 10.1186/1471-2164-8-316, 2072958, 17845718
    • Seemann SE, Gilchrist MJ, Hofacker IL, Stadler PF, Gorodkin J. Detection of RNA structures in porcine EST data and related mammals. BMC Genomics 2007, 8:316. 10.1186/1471-2164-8-316, 2072958, 17845718.
    • (2007) BMC Genomics , vol.8 , pp. 316
    • Seemann, S.E.1    Gilchrist, M.J.2    Hofacker, I.L.3    Stadler, P.F.4    Gorodkin, J.5
  • 43
    • 0242317680 scopus 로고    scopus 로고
    • Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics
    • 10.1093/nar/gkg438, 165953, 12853629
    • McCutcheon JP, Eddy SR. Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. Nucleic Acids Res 2003, 31:4119-4128. 10.1093/nar/gkg438, 165953, 12853629.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4119-4128
    • McCutcheon, J.P.1    Eddy, S.R.2
  • 46
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • 10.1093/nar/gkn923, 2615629, 19033363
    • Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37:1-13. 10.1093/nar/gkn923, 2615629, 19033363.
    • (2009) Nucleic Acids Res , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 47
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 48
    • 0344319833 scopus 로고    scopus 로고
    • Identifying biological themes within lists of genes with EASE
    • 10.1186/gb-2003-4-10-r70, 328459, 14519205
    • Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4:R70. 10.1186/gb-2003-4-10-r70, 328459, 14519205.
    • (2003) Genome Biol , vol.4
    • Hosack, D.A.1    Dennis, G.2    Sherman, B.T.3    Lane, H.C.4    Lempicki, R.A.5
  • 49
    • 38649114329 scopus 로고    scopus 로고
    • Specific expression of long noncoding RNAs in the mouse brain
    • 10.1073/pnas.0706729105, 2206602, 18184812
    • Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 2008, 105:716-721. 10.1073/pnas.0706729105, 2206602, 18184812.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 716-721
    • Mercer, T.R.1    Dinger, M.E.2    Sunkin, S.M.3    Mehler, M.F.4    Mattick, J.S.5
  • 50
    • 77952581350 scopus 로고    scopus 로고
    • Long non-coding RNAs in nervous system function and disease
    • 2883659, 20380817
    • Qureshi IA, Mattick JS, Mehler MF. Long non-coding RNAs in nervous system function and disease. Brain Res 2010, 1338:20-35. 2883659, 20380817.
    • (2010) Brain Res , vol.1338 , pp. 20-35
    • Qureshi, I.A.1    Mattick, J.S.2    Mehler, M.F.3
  • 51
    • 75149163987 scopus 로고    scopus 로고
    • Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells
    • 10.1261/rna.1441510, 2811662, 20026622
    • Sheik Mohamed J, Gaughwin PM, Lim B, Robson P, Lipovich L. Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 2010, 16:324-337. 10.1261/rna.1441510, 2811662, 20026622.
    • (2010) RNA , vol.16 , pp. 324-337
    • Sheik Mohamed, J.1    Gaughwin, P.M.2    Lim, B.3    Robson, P.4    Lipovich, L.5
  • 54
    • 77951891107 scopus 로고    scopus 로고
    • Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements
    • 10.1186/1471-2164-11-151, 2847969, 20202189
    • Licastro D, Gennarino VA, Petrera F, Sanges R, Banfi S, Stupka E. Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements. BMC Genomics 2010, 11:151. 10.1186/1471-2164-11-151, 2847969, 20202189.
    • (2010) BMC Genomics , vol.11 , pp. 151
    • Licastro, D.1    Gennarino, V.A.2    Petrera, F.3    Sanges, R.4    Banfi, S.5    Stupka, E.6
  • 58
    • 63149152651 scopus 로고    scopus 로고
    • The oncoprotein LMO3 interacts with calcium- and integrin-binding protein CIB
    • Hui L, Ji C, Hui B, Lv T, Ha X, Yang J, Cai W. The oncoprotein LMO3 interacts with calcium- and integrin-binding protein CIB. Brain Res 2009, 1265:24-29.
    • (2009) Brain Res , vol.1265 , pp. 24-29
    • Hui, L.1    Ji, C.2    Hui, B.3    Lv, T.4    Ha, X.5    Yang, J.6    Cai, W.7
  • 59
    • 19644363959 scopus 로고    scopus 로고
    • LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma
    • 10.1158/0008-5472.CAN-04-4630, 15930276
    • Aoyama M, Ozaki T, Inuzuka H, Tomotsune D, Hirato J, Okamoto Y, Tokita H, Ohira M, Nakagawara A. LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Cancer Res 2005, 65:4587-4597. 10.1158/0008-5472.CAN-04-4630, 15930276.
    • (2005) Cancer Res , vol.65 , pp. 4587-4597
    • Aoyama, M.1    Ozaki, T.2    Inuzuka, H.3    Tomotsune, D.4    Hirato, J.5    Okamoto, Y.6    Tokita, H.7    Ohira, M.8    Nakagawara, A.9
  • 60
    • 67849095416 scopus 로고    scopus 로고
    • BioMart Central Portal--unified access to biological data
    • 10.1093/nar/gkp265, 2703988, 19420058
    • Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A. BioMart Central Portal--unified access to biological data. Nucleic Acids Res 2009, 37:W23-27. 10.1093/nar/gkp265, 2703988, 19420058.
    • (2009) Nucleic Acids Res , vol.37
    • Haider, S.1    Ballester, B.2    Smedley, D.3    Zhang, J.4    Rice, P.5    Kasprzyk, A.6
  • 61
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated Profile HMM Searches
    • 10.1371/journal.pcbi.1002195, 3197634, 22039361
    • Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol 2011, 7:e1002195. 10.1371/journal.pcbi.1002195, 3197634, 22039361.
    • (2011) PLoS Comput Biol , vol.7
    • Eddy, S.R.1
  • 63
    • 84887205240 scopus 로고    scopus 로고
    • http://www.genome.ucsc.edu/cgi-bin/hgLiftOver
  • 65
    • 27544491192 scopus 로고    scopus 로고
    • ROCR: visualizing classifier performance in R
    • 10.1093/bioinformatics/bti623, 16096348
    • Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics 2005, 21:3940-3941. 10.1093/bioinformatics/bti623, 16096348.
    • (2005) Bioinformatics , vol.21 , pp. 3940-3941
    • Sing, T.1    Sander, O.2    Beerenwinkel, N.3    Lengauer, T.4
  • 66
    • 47249140906 scopus 로고    scopus 로고
    • Dinucleotide controlled null models for comparative RNA gene prediction
    • 10.1186/1471-2105-9-248, 2453142, 18505553
    • Gesell T, Washietl S. Dinucleotide controlled null models for comparative RNA gene prediction. BMC Bioinformatics 2008, 9:248. 10.1186/1471-2105-9-248, 2453142, 18505553.
    • (2008) BMC Bioinformatics , vol.9 , pp. 248
    • Gesell, T.1    Washietl, S.2
  • 68
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • 10.1093/bioinformatics/btq033, 2832824, 20110278
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842. 10.1093/bioinformatics/btq033, 2832824, 20110278.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 69
    • 59949096873 scopus 로고    scopus 로고
    • EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    • 2652215, 19029536
    • Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 2009, 19:327-335. 2652215, 19029536.
    • (2009) Genome Res , vol.19 , pp. 327-335
    • Vilella, A.J.1    Severin, J.2    Ureta-Vidal, A.3    Heng, L.4    Durbin, R.5    Birney, E.6
  • 70
    • 84887177925 scopus 로고    scopus 로고
    • http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/all_est.txt.gz
  • 71
    • 84887163227 scopus 로고    scopus 로고
    • http://hgdownload.cse.ucsc.edu/goldenPath/danRer7/database/all_est.txt.gz
  • 73
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • 10.1093/bioinformatics/btp120, 2672628, 19289445
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111. 10.1093/bioinformatics/btp120, 2672628, 19289445.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.