메뉴 건너뛰기




Volumn 29, Issue 20, 2013, Pages 2539-2546

Oncofuse: A computational framework for the prediction of the oncogenic potential of gene fusions

Author keywords

[No Author keywords available]

Indexed keywords

BAYES THEOREM; GENE EXPRESSION PROFILING; GENE FUSION; GENETIC DATABASE; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; NEOPLASM; ONCOGENE; PROCEDURES; ARTICLE; METHODOLOGY;

EID: 84885588233     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt445     Document Type: Article
Times cited : (82)

References (34)
  • 1
    • 30044431810 scopus 로고    scopus 로고
    • Transcription-mediated gene fusion in the human genome
    • Akiva, P. et al. (2006) Transcription-mediated gene fusion in the human genome. Genome Res., 16, 30-36
    • (2006) Genome Res , vol.16 , pp. 30-36
    • Akiva, P.1
  • 2
    • 84860117771 scopus 로고    scopus 로고
    • Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer
    • Asmann, Y.W. et al. (2012) Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer. Cancer Res., 72, 1921-1928
    • (2012) Cancer Res , vol.72 , pp. 1921-1928
    • Asmann, Y.W.1
  • 3
    • 84870815979 scopus 로고    scopus 로고
    • Discovering chimeric transcripts in paired-end RNA-seq data by using Ericscript
    • Benelli, M. et al. (2012) Discovering chimeric transcripts in paired-end RNA-seq data by using Ericscript. Bioinformatics, 28, 3232-3239
    • (2012) Bioinformatics , vol.28 , pp. 3232-3239
    • Benelli, M.1
  • 4
    • 78249261016 scopus 로고    scopus 로고
    • Accumulation of driver and passenger mutations during tumor progression
    • Bozic, I. et al. (2010) Accumulation of driver and passenger mutations during tumor progression. Proc. Natl Acad. Sci. USA, 107, 18545-18550
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 18545-18550
    • Bozic, I.1
  • 5
    • 78651486046 scopus 로고    scopus 로고
    • Identification of fusion genes in breast cancer by paired-end RNA-sequencing
    • Edgren, H. et al. (2011) Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol., 12, R6
    • (2011) Genome Biol , vol.12
    • Edgren, H.1
  • 6
    • 84863009996 scopus 로고    scopus 로고
    • FusionFinder: A software tool to identify expressed gene fusion candidates from RNA-Seq data
    • Francis, R.W. et al. (2012) FusionFinder: A software tool to identify expressed gene fusion candidates from RNA-Seq data. PLoS One, 7, e39987
    • (2012) PLoS One , vol.7
    • Francis, R.W.1
  • 7
    • 7244250182 scopus 로고    scopus 로고
    • Data mining in bioinformatics using Weka
    • Frank, E. et al. (2004) Data mining in bioinformatics using Weka. Bioinformatics, 20, 2479-2481
    • (2004) Bioinformatics , vol.20 , pp. 2479-2481
    • Frank, E.1
  • 8
    • 84863512195 scopus 로고    scopus 로고
    • Novel domain combinations in proteins encoded by chimeric transcripts
    • Frenkel-Morgenstern, M. and Valencia, A. (2012) Novel domain combinations in proteins encoded by chimeric transcripts. Bioinformatics, 28, i67-i74
    • (2012) Bioinformatics , vol.28
    • Frenkel-Morgenstern, M.1    Valencia, A.2
  • 9
    • 84863541698 scopus 로고    scopus 로고
    • Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts
    • Frenkel-Morgenstern, M. et al. (2012) Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts. Genome Res., 22, 1231-1242
    • (2012) Genome Res , vol.22 , pp. 1231-1242
    • Frenkel-Morgenstern, M.1
  • 10
    • 1542515338 scopus 로고    scopus 로고
    • A census of human cancer genes
    • Futreal, P.A. et al. (2004) A census of human cancer genes. Nat. Rev. Cancer, 4, 177-183
    • (2004) Nat. Rev. Cancer , vol.4 , pp. 177-183
    • Futreal, P.A.1
  • 11
    • 83455220210 scopus 로고    scopus 로고
    • Nup98 gene fusions and hematopoietic malignancies: Common themes and new biologic insights
    • Gough, S.M. et al. (2011) NUP98 gene fusions and hematopoietic malignancies: Common themes and new biologic insights. Blood, 118, 6247-6257
    • (2011) Blood , vol.118 , pp. 6247-6257
    • Gough, S.M.1
  • 12
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • Hanahan, D. and Weinberg, R.A. (2000) The hallmarks of cancer. Cell, 100, 57-70
    • (2000) Cell , vol.100 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 13
    • 79952284127 scopus 로고    scopus 로고
    • Hallmarks of cancer: The next generation
    • Hanahan, D. and Weinberg, R.A. (2011) Hallmarks of cancer: The next generation. Cell, 144, 646-674
    • (2011) Cell , vol.144 , pp. 646-674
    • Hanahan, D.1    Weinberg, R.A.2
  • 14
    • 73549101052 scopus 로고    scopus 로고
    • Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins
    • Hegyi, H. et al. (2009) Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins. PLoS Comput. Biol., 5, e1000552
    • (2009) PLoS Comput. Biol , vol.5
    • Hegyi, H.1
  • 15
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D.W. et al. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57
    • (2009) Nat. Protoc , vol.4 , pp. 44-57
    • Huang, D.W.1
  • 16
    • 84858602406 scopus 로고    scopus 로고
    • InterPro in 2011: New developments in the family and domain prediction database
    • Hunter, S. et al. (2012) InterPro in 2011: New developments in the family and domain prediction database. Nucleic Acids Res., 40, D306-D312
    • (2012) Nucleic Acids Res , vol.40
    • Hunter, S.1
  • 17
    • 80051507403 scopus 로고    scopus 로고
    • Tophat-fusion: An algorithm for discovery of novel fusion transcripts
    • Kim, D. and Salzberg, S.L. (2011) TopHat-Fusion: An algorithm for discovery of novel fusion transcripts. Genome Biol., 12, R72
    • (2011) Genome Biol , vol.12
    • Kim, D.1    Salzberg, S.L.2
  • 18
    • 75549092352 scopus 로고    scopus 로고
    • ChimerDB 2.0-A knowledgebase for fusion genes updated
    • Kim, P. et al. (2010) ChimerDB 2.0-A knowledgebase for fusion genes updated. Nucleic Acids Res., 38, D81-D85
    • (2010) Nucleic Acids Res , vol.38
    • Kim, P.1
  • 19
    • 84655169623 scopus 로고    scopus 로고
    • Epithelial cell polarity, stem cells and cancer
    • Martin-Belmonte, F. and Perez-Moreno, M. (2012) Epithelial cell polarity, stem cells and cancer. Nat. Rev. Cancer, 12, 23-38
    • (2012) Nat. Rev. Cancer , vol.12 , pp. 23-38
    • Martin-Belmonte, F.1    Perez-Moreno, M.2
  • 20
    • 33947581390 scopus 로고    scopus 로고
    • The impact of translocations and gene fusions on cancer causation
    • Mitelman, F. et al. (2007) The impact of translocations and gene fusions on cancer causation. Nat. Rev. Cancer, 7, 233-245
    • (2007) Nat. Rev. Cancer , vol.7 , pp. 233-245
    • Mitelman, F.1
  • 21
    • 78751650428 scopus 로고    scopus 로고
    • Deep rna sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples
    • Nacu, S. et al. (2011) Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC Med. Genomics, 4, 11
    • (2011) BMC Med. Genomics , vol.4 , pp. 11
    • Nacu, S.1
  • 22
    • 56049124569 scopus 로고    scopus 로고
    • Chromosomal translocations in cancer
    • Nambiar, M. et al. (2008) Chromosomal translocations in cancer. Biochim. Biophys. Acta, 1786, 139-152
    • (2008) Biochim. Biophys. Acta , vol.1786 , pp. 139-152
    • Nambiar, M.1
  • 23
    • 33846910723 scopus 로고    scopus 로고
    • TICdb: A collection of gene-mapped translocation breakpoints in cancer
    • Novo, F.J. et al. (2007) TICdb: A collection of gene-mapped translocation breakpoints in cancer. BMC Genomics, 8, 33
    • (2007) BMC Genomics , vol.8 , pp. 33
    • Novo, F.J.1
  • 24
    • 65449183174 scopus 로고    scopus 로고
    • Signatures of selection in fusion transcripts resulting from chromosomal translocations in human cancer
    • Ortiz de Mendíbil, I. et al. (2009) Signatures of selection in fusion transcripts resulting from chromosomal translocations in human cancer. PloS One, 4, e4805
    • (2009) PloS One , vol.4
    • Ortiz De Mendíbil, I.1
  • 25
    • 30044445670 scopus 로고    scopus 로고
    • Tandem chimerism as a means to increase protein complexity in the human genome
    • Parra, G. et al. (2006) Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res., 16, 37-44
    • (2006) Genome Res , vol.16 , pp. 37-44
    • Parra, G.1
  • 26
    • 0027970838 scopus 로고
    • Chromosomal translocations in human cancer
    • Rabbitts, T.H. (1994) Chromosomal translocations in human cancer. Nature, 372, 143-149
    • (1994) Nature , vol.372 , pp. 143-149
    • Rabbitts, T.H.1
  • 27
    • 14644425319 scopus 로고    scopus 로고
    • Mechanisms of BCR-ABL in the pathogenesis of chronic myelogenous leukaemia
    • Ren, R. (2005) Mechanisms of BCR-ABL in the pathogenesis of chronic myelogenous leukaemia. Nat. Rev. Cancer, 5, 172-183
    • (2005) Nat. Rev. Cancer , vol.5 , pp. 172-183
    • Ren, R.1
  • 28
    • 84858288121 scopus 로고    scopus 로고
    • Clinical potential of the ERG oncoprotein in prostate cancer
    • Rosen, P. et al. (2012) Clinical potential of the ERG oncoprotein in prostate cancer. Nat. Rev. Urol., 9, 131-137
    • (2012) Nat. Rev. Urol , vol.9 , pp. 131-137
    • Rosen, P.1
  • 29
    • 84861141246 scopus 로고    scopus 로고
    • RNA-Seq mapping and detection of gene fusions with a suffix array algorithm
    • Sakarya, O. et al. (2012) RNA-Seq mapping and detection of gene fusions with a suffix array algorithm. PLoS Comput. Biol., 8, e1002464
    • (2012) PLoS Comput. Biol , vol.8
    • Sakarya, O.1
  • 30
    • 84872009827 scopus 로고    scopus 로고
    • Genomic hallmarks of genes involved in chromosomal translocations in hematological cancer
    • Shugay, M. et al. (2012) Genomic hallmarks of genes involved in chromosomal translocations in hematological cancer. PLoS Comput. Biol., 8, e1002797
    • (2012) PLoS Comput. Biol , vol.8
    • Shugay, M.1
  • 31
    • 84869455546 scopus 로고    scopus 로고
    • A novel missense-mutation-related feature extraction scheme for driver mutation identification
    • Tan, H. et al. (2012) A novel missense-mutation-related feature extraction scheme for driver mutation identification. Bioinformatics, 28, 2948-2955
    • (2012) Bioinformatics , vol.28 , pp. 2948-2955
    • Tan, H.1
  • 33
    • 84875490185 scopus 로고    scopus 로고
    • Cancer genome landscapes
    • Vogelstein, B. et al. (2013) Cancer genome landscapes. Science, 339, 1546-1558
    • (2013) Science , vol.339 , pp. 1546-1558
    • Vogelstein, B.1
  • 34
    • 70449375354 scopus 로고    scopus 로고
    • An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer
    • Wang, X.S. et al. (2009) An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nat. Biotechnol., 27, 1005-1011
    • (2009) Nat. Biotechnol , vol.27 , pp. 1005-1011
    • Wang, X.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.