메뉴 건너뛰기




Volumn 8, Issue 1, 2015, Pages

Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data

Author keywords

Cancer; Gene expression; Next generation sequencing

Indexed keywords

ARTICLE; CANCER CELL LINE; CELL DIFFERENTIATION; CELL TRANSFORMATION; EMBRYONIC STEM CELL; ENDOGENOUS RETROVIRUS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE LOCUS; GENETIC CODE; HOUSEKEEPING GENE; HUMAN; HUMAN CELL; MOLECULAR GENETICS; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; TRANSCRIPTION REGULATION; UPREGULATION; CELL LINE; ESSENTIAL GENE; GENETIC DATABASE; GENETICS; METABOLISM; SEQUENCE ANALYSIS;

EID: 84945901609     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/s12920-015-0146-5     Document Type: Article
Times cited : (17)

References (39)
  • 1
    • 0034917315 scopus 로고    scopus 로고
    • Endogenous retroviruses in the human genome sequence
    • reviews1017-reviews1017.5
    • Griffiths D: Endogenous retroviruses in the human genome sequence. Genome Biology 2001, 2(6):reviews1017-reviews1017.5
    • (2001) Genome Biology , vol.2 , Issue.6
    • Griffiths, D.1
  • 2
    • 84867050577 scopus 로고    scopus 로고
    • Transposable elements: An abundant and natural source of regulatory sequences for host genes
    • Rebollo R, Romanish MT, Mager DL. Transposable elements: An abundant and natural source of regulatory sequences for host genes. Annu Rev Genet. 2012;46:21-42.
    • (2012) Annu Rev Genet. , vol.46 , pp. 21-42
    • Rebollo, R.1    Romanish, M.T.2    Mager, D.L.3
  • 4
    • 38049097957 scopus 로고    scopus 로고
    • Placental syncytins: Genetic disjunction between the fusogenic and immunosuppressive activity of retroviral envelope proteins
    • Mangeney M, Renard M, Schlecht-Louf G, Bouallaga I, Heidmann O, Letzelter C, et al. Placental syncytins: Genetic disjunction between the fusogenic and immunosuppressive activity of retroviral envelope proteins. Proc Natl Acad Sci U S A. 2007;104(51):20534-9.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , Issue.51 , pp. 20534-20539
    • Mangeney, M.1    Renard, M.2    Schlecht-Louf, G.3    Bouallaga, I.4    Heidmann, O.5    Letzelter, C.6
  • 5
    • 0342545919 scopus 로고    scopus 로고
    • Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis
    • Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, et al. Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature. 2000;403(6771):785-9.
    • (2000) Nature , vol.403 , Issue.6771 , pp. 785-789
    • Mi, S.1    Lee, X.2    Li, X.3    Veldman, G.M.4    Finnerty, H.5    Racie, L.6
  • 6
    • 0842308211 scopus 로고    scopus 로고
    • HERV-W-related RNA detected in plasma from individuals with recent-onset schizophrenia or schizoaffective disorder
    • Karlsson H, Schröder J, Bachmann S, Bottmer C, Yolken RH. HERV-W-related RNA detected in plasma from individuals with recent-onset schizophrenia or schizoaffective disorder. Mol Psychiatry. 2004;9(1):12-3.
    • (2004) Mol Psychiatry , vol.9 , Issue.1 , pp. 12-13
    • Karlsson, H.1    Schröder, J.2    Bachmann, S.3    Bottmer, C.4    Yolken, R.H.5
  • 7
    • 0034796287 scopus 로고    scopus 로고
    • Endogenous retroviruses and multiple sclerosis
    • Kolson DL, Gonzalez-Scarano F. Endogenous retroviruses and multiple sclerosis. Ann Neurol. 2001;50(4):429-30.
    • (2001) Ann Neurol. , vol.50 , Issue.4 , pp. 429-430
    • Kolson, D.L.1    Gonzalez-Scarano, F.2
  • 8
    • 33746152795 scopus 로고    scopus 로고
    • Expression of the human endogenous retrovirus-K transmembrane envelope, rec and Np9 proteins in melanomas and melanoma cell lines
    • Buscher K, Hahn S, Hofmann M, Trefzer U, Ozel M, Sterry W, et al. Expression of the human endogenous retrovirus-K transmembrane envelope, Rec and Np9 proteins in melanomas and melanoma cell lines. Melanoma Res. 2006;16(3):223-34.
    • (2006) Melanoma Res. , vol.16 , Issue.3 , pp. 223-234
    • Buscher, K.1    Hahn, S.2    Hofmann, M.3    Trefzer, U.4    Ozel, M.5    Sterry, W.6
  • 9
    • 38849133558 scopus 로고    scopus 로고
    • Variable transcriptional activity of endogenous retroviruses in human breast cancer
    • Frank O, Verbeke C, Schwarz N, Mayer J, Fabarius A, Hehlmann R, et al. Variable transcriptional activity of endogenous retroviruses in human breast cancer. J Virol. 2008;82(4):1808-18.
    • (2008) J Virol. , vol.82 , Issue.4 , pp. 1808-1818
    • Frank, O.1    Verbeke, C.2    Schwarz, N.3    Mayer, J.4    Fabarius, A.5    Hehlmann, R.6
  • 11
    • 10644240714 scopus 로고    scopus 로고
    • Comprehensive analysis of human endogenous retrovirus transcriptional activity in human tissues with a retrovirus-specific microarray
    • Seifarth W, Frank O, Zeilfelder U, Spiess B, Greenwood AD, Hehlmann R, et al. Comprehensive Analysis of Human Endogenous Retrovirus Transcriptional Activity in Human Tissues with a Retrovirus-Specific Microarray. J Virol. 2005;79(1):341-52.
    • (2005) J Virol. , vol.79 , Issue.1 , pp. 341-352
    • Seifarth, W.1    Frank, O.2    Zeilfelder, U.3    Spiess, B.4    Greenwood, A.D.5    Hehlmann, R.6
  • 12
    • 57749195712 scopus 로고    scopus 로고
    • RNA-seq: A revolutionary tool for transcriptomics
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57-63.
    • (2009) Nat Rev Genet. , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 13
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia of DNA elements) project
    • The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004;306(5696):636-40.
    • (2004) Science , vol.306 , Issue.5696 , pp. 636-640
  • 15
  • 16
    • 84865858631 scopus 로고    scopus 로고
    • RNA editing in the human ENCODE RNA-seq data
    • Park E, Williams B, Wold BJ, Mortazavi A. RNA editing in the human ENCODE RNA-seq data. Genome Res. 2012;22(9):1626-33.
    • (2012) Genome Res. , vol.22 , Issue.9 , pp. 1626-1633
    • Park, E.1    Williams, B.2    Wold, B.J.3    Mortazavi, A.4
  • 17
    • 84865839598 scopus 로고    scopus 로고
    • Long noncoding RNAs are rarely translated in two human cell lines
    • Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE, et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 2012;22(9):1646-57.
    • (2012) Genome Res. , vol.22 , Issue.9 , pp. 1646-1657
    • Bánfai, B.1    Jia, H.2    Khatun, J.3    Wood, E.4    Risk, B.5    Gundling, W.E.6
  • 19
    • 84904086862 scopus 로고    scopus 로고
    • Transcriptional landscape of repetitive elements in normal and cancer human cells
    • Criscione S, Zhang Y, Thompson W, Sedivy J, Neretti N. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genomics. 2014;15(1):583.
    • (2014) BMC Genomics , vol.15 , Issue.1 , pp. 583
    • Criscione, S.1    Zhang, Y.2    Thompson, W.3    Sedivy, J.4    Neretti, N.5
  • 20
    • 84898010302 scopus 로고    scopus 로고
    • The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
    • Lu X, Sachs F, Ramsay L, Jacques PE, Göke J, Bourque G, et al. The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol. 2014;21:423-5.
    • (2014) Nat Struct Mol Biol. , vol.21 , pp. 423-425
    • Lu, X.1    Sachs, F.2    Ramsay, L.3    Jacques, P.E.4    Göke, J.5    Bourque, G.6
  • 21
    • 0036088127 scopus 로고    scopus 로고
    • HERVd: Database of human endogenous retroviruses
    • Pačes J, Pavlíček A, Pačes V. HERVd: database of human endogenous retroviruses. Nucleic Acids Res. 2002;30(1):205-6.
    • (2002) Nucleic Acids Res. , vol.30 , Issue.1 , pp. 205-206
    • Pačes, J.1    Pavlíček, A.2    Pačes, V.3
  • 23
    • 84874287845 scopus 로고    scopus 로고
    • Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-seq technique
    • Gao Y, Xu H, Shen Y, Wang J. Transcriptomic analysis of rice (Oryza sativa) endosperm using the RNA-Seq technique. Plant Mol Biol. 2013;81(4-5):363-78.
    • (2013) Plant Mol Biol. , vol.81 , Issue.4-5 , pp. 363-378
    • Gao, Y.1    Xu, H.2    Shen, Y.3    Wang, J.4
  • 24
    • 84906935851 scopus 로고    scopus 로고
    • Exploring differentially expressed genes in the ovaries of uniparous and multiparous goats using the RNA-seq (Quantification) method
    • Ling YH, Xiang H, Li YS, Liu Y, Zhang YH, Zhang ZJ, et al. Exploring differentially expressed genes in the ovaries of uniparous and multiparous goats using the RNA-Seq (Quantification) method. Gene. 2014;550(1):148-53.
    • (2014) Gene. , vol.550 , Issue.1 , pp. 148-153
    • Ling, Y.H.1    Xiang, H.2    Li, Y.S.3    Liu, Y.4    Zhang, Y.H.5    Zhang, Z.J.6
  • 25
    • 0029129017 scopus 로고
    • Isolation of novel human endogenous retrovirus-like elements with foamy virus-related pol sequence
    • Cordonnier A, Casella JF, Heidmann T. Isolation of novel human endogenous retrovirus-like elements with foamy virus-related pol sequence. J Virol. 1995;69(9):5890-7.
    • (1995) J Virol. , vol.69 , Issue.9 , pp. 5890-5897
    • Cordonnier, A.1    Casella, J.F.2    Heidmann, T.3
  • 29
    • 84871215627 scopus 로고    scopus 로고
    • HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency
    • Santoni F, Guerra J, Luban J. HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Retrovirology. 2012;9(1):111.
    • (2012) Retrovirology , vol.9 , Issue.1 , pp. 111
    • Santoni, F.1    Guerra, J.2    Luban, J.3
  • 30
    • 70450170839 scopus 로고    scopus 로고
    • Human endogenous retroviral long terminal repeat sequences as cell type-specific promoters in retroviral vectors
    • Schön U, Diem O, Leitner L, Gunzburg WH, Mager DL, Salmons B, et al. Human endogenous retroviral long terminal repeat sequences as cell type-specific promoters in retroviral vectors. J Virol. 2009;83(23):12643-50.
    • (2009) J Virol. , vol.83 , Issue.23 , pp. 12643-12650
    • Schön, U.1    Diem, O.2    Leitner, L.3    Gunzburg, W.H.4    Mager, D.L.5    Salmons, B.6
  • 31
    • 84891814834 scopus 로고    scopus 로고
    • Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC genome browser
    • Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, et al. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics. 2014;30(7):1003-5.
    • (2014) Bioinformatics , vol.30 , Issue.7 , pp. 1003-1005
    • Raney, B.J.1    Dreszer, T.R.2    Barber, G.P.3    Clawson, H.4    Fujita, P.A.5    Wang, T.6
  • 33
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-The BLAST-like alignment tool
    • Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res. 2002;12(4):656-64.
    • (2002) Genome Res. , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 34
    • 84897397058 scopus 로고    scopus 로고
    • Feature counts: An efficient general purpose program for assigning sequence reads to genomic features
    • Liao Y, Smyth GK, Shi W. feature Counts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923-30.
    • (2014) Bioinformatics , vol.30 , Issue.7 , pp. 923-930
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 35
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2
  • 38
    • 84988674410 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J R Stat Soc Ser B Methodol. 1995;57(1):289-300.
    • (1995) J R Stat Soc ser B Methodol. , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 39
    • 84884416048 scopus 로고    scopus 로고
    • Human housekeeping genes, revisited
    • Eisenberg E, Levanon EY. Human housekeeping genes, revisited. Trends Genet. 2013;29(10):569-74.
    • (2013) Trends Genet. , vol.29 , Issue.10 , pp. 569-574
    • Eisenberg, E.1    Levanon, E.Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.