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Volumn 42, Issue 15, 2014, Pages e121-

SpliceNet: Recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; MITOGEN ACTIVATED PROTEIN KINASE; PROTEIN BCL X; RNA; ISOPROTEIN;

EID: 84959852049     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku577     Document Type: Article
Times cited : (19)

References (45)
  • 1
    • 7444220147 scopus 로고    scopus 로고
    • Aberrant and alternative splicing in cancer
    • Venables, J.P. (2004) Aberrant and alternative splicing in cancer. Cancer Res., 64, 7647-7654.
    • (2004) Cancer Res , vol.64 , pp. 7647-7654
    • Venables, J.P.1
  • 2
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cells functional organization
    • Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cells functional organization. Nat. Rev. Genet., 5, U101-U115.
    • (2004) Nat. Rev. Genet , vol.5 , pp. U101-U115
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 3
    • 84893319771 scopus 로고    scopus 로고
    • DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment
    • Yalamanchili, H.K., Yan, B., Li, M.J., Qin, J., Zhao, Z., Chin, F.Y. and Wang, J. (2014) DDGni: dynamic delay gene-network inference from high-temporal data using gapped local alignment. Bioinformatics, 30, 377-383.
    • (2014) Bioinformatics , vol.30 , pp. 377-383
    • Yalamanchili, H.K.1    Yan, B.2    Li, M.J.3    Qin, J.4    Zhao, Z.5    Chin, F.Y.6    Wang, J.7
  • 4
    • 77952310528 scopus 로고    scopus 로고
    • A human functional protein interaction network and its application to cancer data analysis
    • Wu, G.M., Feng, X. and Stein, L. (2010) A human functional protein interaction network and its application to cancer data analysis. Genome Biol., 11, R53.
    • (2010) Genome Biol , vol.11 , pp. R53
    • Wu, G.M.1    Feng, X.2    Stein, L.3
  • 5
    • 0034927555 scopus 로고    scopus 로고
    • Analysis of variance for gene expression microarray data
    • Kerr, M.K., Martin, M. and Churchill, G.A. (2000) Analysis of variance for gene expression microarray data. J. Comput. Biol., 7, 819-837.
    • (2000) J. Comput. Biol , vol.7 , pp. 819-837
    • Kerr, M.K.1    Martin, M.2    Churchill, G.A.3
  • 8
    • 84887617966 scopus 로고    scopus 로고
    • Opportunities and methods for studying alternative splicing in cancer with RNA-Seq
    • Feng, H., Qin, Z. and Zhang, X. (2012) Opportunities and methods for studying alternative splicing in cancer with RNA-Seq. Cancer Lett. 340, 179-191.
    • (2012) Cancer Lett. , vol.340 , pp. 179-191
    • Feng, H.1    Qin, Z.2    Zhang, X.3
  • 9
    • 84875807798 scopus 로고    scopus 로고
    • A novel neural response algorithm for protein function prediction
    • Yalamanchili, H.K., Xiao, Q.W. and Wang, J. (2012) A novel neural response algorithm for protein function prediction. BMC Syst. Biol., 6(Suppl. 1), S19.
    • (2012) BMC Syst. Biol , vol.6 , pp. S19
    • Yalamanchili, H.K.1    Xiao, Q.W.2    Wang, J.3
  • 10
    • 18344364099 scopus 로고    scopus 로고
    • Understanding alternative splicing: Towards a cellular code
    • Matlin, A.J., Clark, F. and Smith, C.W. (2005) Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol., 6, 386-398.
    • (2005) Nat. Rev. Mol. Cell Biol , vol.6 , pp. 386-398
    • Matlin, A.J.1    Clark, F.2    Smith, C.W.3
  • 12
    • 0043136678 scopus 로고    scopus 로고
    • Alternative splicing disrupts a nuclear localization signal in spleen tyrosine kinase that is required for invasion suppression in breast cancer
    • Wang, L., Duke, L., Zhang, P.S., Arlinghaus, R.B., Symmans, W.F., Sahin, A., Mendez, R. and Dai, J.L. (2003) Alternative splicing disrupts a nuclear localization signal in spleen tyrosine kinase that is required for invasion suppression in breast cancer. Cancer Res., 63, 4724-4730.
    • (2003) Cancer Res , vol.63 , pp. 4724-4730
    • Wang, L.1    Duke, L.2    Zhang, P.S.3    Arlinghaus, R.B.4    Symmans, W.F.5    Sahin, A.6    Mendez, R.7    Dai, J.L.8
  • 13
    • 77951718967 scopus 로고    scopus 로고
    • Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers
    • Menon, R. and Omenn, G.S. (2010) Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers. Cancer Res., 70, 3440-3449.
    • (2010) Cancer Res , vol.70 , pp. 3440-3449
    • Menon, R.1    Omenn, G.S.2
  • 14
    • 77957338139 scopus 로고    scopus 로고
    • Evolution of peroxisome proliferator-activated receptor gamma alternative splicing
    • Dou, T., Xu, J., Gao, Y., Gu, J., Ji, C., Xie, Y. and Zhou, Y. (2010) Evolution of peroxisome proliferator-activated receptor gamma alternative splicing. Front. Biosci., 2, 1334-1343.
    • (2010) Front. Biosci , vol.2 , pp. 1334-1343
    • Dou, T.1    Xu, J.2    Gao, Y.3    Gu, J.4    Ji, C.5    Xie, Y.6    Zhou, Y.7
  • 15
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
    • (2009) Nat. Rev. Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 18
    • 84877249559 scopus 로고    scopus 로고
    • Canonical correlation analysis for RNA-seq co-expression networks
    • Hong, S., Chen, X., Jin, L. and Xiong, M. (2013) Canonical correlation analysis for RNA-seq co-expression networks. Nucleic Acids Res., 41, e95.
    • (2013) Nucleic Acids Res , vol.41 , pp. e95
    • Hong, S.1    Chen, X.2    Jin, L.3    Xiong, M.4
  • 19
    • 84859466792 scopus 로고    scopus 로고
    • Likelihood ratio test for detecting gene (G)-environment (E) interactions under an additive risk model exploiting G-E independence for case-control data
    • Han, S.S., Rosenberg, P.S., Garcia-Closas, M., Figueroa, J.D., Silverman, D., Chanock, S.J., Rothman, N. and Chatterjee, N. (2012) Likelihood ratio test for detecting gene (G)-environment (E) interactions under an additive risk model exploiting G-E independence for case-control data. Am. J. Epidemiol., 176, 1060-1067.
    • (2012) Am. J. Epidemiol , vol.176 , pp. 1060-1067
    • Han, S.S.1    Rosenberg, P.S.2    Garcia-Closas, M.3    Figueroa, J.D.4    Silverman, D.5    Chanock, S.J.6    Rothman, N.7    Chatterjee, N.8
  • 20
    • 79957842166 scopus 로고    scopus 로고
    • Computational methods for transcriptome annotation and quantification using RNA-seq
    • Garber, M., Grabherr, M.G., Guttman, M. and Trapnell, C. (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods, 8, 469-477.
    • (2011) Nat. Methods , vol.8 , pp. 469-477
    • Garber, M.1    Grabherr, M.G.2    Guttman, M.3    Trapnell, C.4
  • 21
    • 84880220238 scopus 로고    scopus 로고
    • Differential network analysis for the identification of condition-specific pathway activity and regulation
    • Gambardella, G., Moretti, M.N., de Cegli, R., Cardone, L., Peron, A. and di Bernardo, D. (2013) Differential network analysis for the identification of condition-specific pathway activity and regulation. Bioinformatics, 29, 1776-1785.
    • (2013) Bioinformatics , vol.29 , pp. 1776-1785
    • Gambardella, G.1    Moretti, M.N.2    De Cegli, R.3    Cardone, L.4    Peron, A.5    Di Bernardo, D.6
  • 22
    • 33745858656 scopus 로고    scopus 로고
    • Positive autoregulation of the transcription factor Pax6 in response to increased levels of either of its major isoforms, Pax6 or Pax6(5a), in cultured cells
    • Pinson, J., Simpson, T.I., O Mason, J. and Price, D.J. (2006) Positive autoregulation of the transcription factor Pax6 in response to increased levels of either of its major isoforms, Pax6 or Pax6(5a), in cultured cells. BMC Dev. Biol., 6, 25.
    • (2006) BMC Dev. Biol , vol.6 , pp. 25
    • Pinson, J.1    Simpson, T.I.2    Mason J, O.3    Price, D.J.4
  • 23
    • 78751570979 scopus 로고    scopus 로고
    • RNA sequencing: Advances, challenges and opportunities
    • Ozsolak, F. and Milos, P.M. (2011) RNA sequencing: advances, challenges and opportunities. Nat. Rev. Genet., 12, 87-98.
    • (2011) Nat. Rev. Genet , vol.12 , pp. 87-98
    • Ozsolak, F.1    Milos, P.M.2
  • 24
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 25
    • 46049110099 scopus 로고    scopus 로고
    • TiGER: A database for tissue-specific gene expression and regulation
    • Liu, X., Yu, X.P., Zack, D.J., Zhu, H. and Qian, J. (2008) TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinformatics, 9, 271.
    • (2008) BMC Bioinformatics , vol.9 , pp. 271
    • Liu, X.1    Yu, X.P.2    Zack, D.J.3    Zhu, H.4    Qian, J.5
  • 28
    • 0031921640 scopus 로고    scopus 로고
    • Statistical features of human exons and their flanking regions
    • Zhang, M.Q. (1998) Statistical features of human exons and their flanking regions. Hum. Mol. Genet., 7, 919-932.
    • (1998) Hum. Mol. Genet , vol.7 , pp. 919-932
    • Zhang, M.Q.1
  • 29
    • 84871934307 scopus 로고    scopus 로고
    • Testing the independence of sets of large-dimensional variables
    • Jiang, D.D., Bai, Z.D. and Zheng, S.R. (2013) Testing the independence of sets of large-dimensional variables. Sci. China Math., 56, 135-147.
    • (2013) Sci. China Math , vol.56 , pp. 135-147
    • Jiang, D.D.1    Bai, Z.D.2    Zheng, S.R.3
  • 30
    • 84864758525 scopus 로고    scopus 로고
    • Evaluation: From precision, recall and F-factor to ROC, informedness, markedness & correlation
    • Powers, D.W.M. (2007) Evaluation: from precision, recall and F-factor to ROC, informedness, markedness & correlation. J. Mach. Learn. Technol., 2 , 37-63.
    • (2007) J. Mach. Learn. Technol , vol.2 , pp. 37-63
    • Powers, D.W.M.1
  • 32
    • 37149011077 scopus 로고    scopus 로고
    • Emetine regulates the alternative splicing of Bcl-x through a protein phosphatase 1-dependent mechanism
    • Boon-Unge, K., Yu, Q.M., Zou, T., Zhou, A., Govitrapong, P. and Zhou, J.H. (2007) Emetine regulates the alternative splicing of Bcl-x through a protein phosphatase 1-dependent mechanism. Chem. Biol., 14, 1386-1392.
    • (2007) Chem. Biol , vol.14 , pp. 1386-1392
    • Boon-Unge, K.1    Yu, Q.M.2    Zou, T.3    Zhou, A.4    Govitrapong, P.5    Zhou, J.H.6
  • 35
    • 0032521183 scopus 로고    scopus 로고
    • Expression of CD44 variant exon 6 in stage i non-small cell lung carcinoma as a prognostic factor
    • Hirata, T., Fukuse, T., Naiki, H., Hitomi, S. and Wada, H. (1998) Expression of CD44 variant exon 6 in stage I non-small cell lung carcinoma as a prognostic factor. Cancer Res., 58, 1108-1110.
    • (1998) Cancer Res , vol.58 , pp. 1108-1110
    • Hirata, T.1    Fukuse, T.2    Naiki, H.3    Hitomi, S.4    Wada, H.5
  • 36
    • 0343081072 scopus 로고    scopus 로고
    • C-CAM1, a candidate tumor suppressor gene, is abnormally expressed in primary lung cancers
    • Wang, L., Lin, S.H., Wu, W.G., Kemp, B.L., Walsh, G.L., Hong, W.K. and Mao, L. (2000) C-CAM1, a candidate tumor suppressor gene, is abnormally expressed in primary lung cancers. Clin. Cancer Res., 6, 2988-2993.
    • (2000) Clin. Cancer Res , vol.6 , pp. 2988-2993
    • Wang, L.1    Lin, S.H.2    Wu, W.G.3    Kemp, B.L.4    Walsh, G.L.5    Hong, W.K.6    Mao, L.7
  • 38
    • 84883483017 scopus 로고    scopus 로고
    • MRNA splicing variants: Exploiting modularity to outwit cancer therapy
    • Dehm, S.M. (2013) mRNA splicing variants: exploiting modularity to outwit cancer therapy. Cancer Res., 73, 5309-5314.
    • (2013) Cancer Res , vol.73 , pp. 5309-5314
    • Dehm, S.M.1
  • 41
    • 77953005066 scopus 로고    scopus 로고
    • Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
    • Pio, R., Blanco, D., Pajares, M.J., Aibar, E., Durany, O., Ezponda, T., Agorreta, J., Gomez-Roman, J., Anton, M.A., Rubio, A. et al. (2010) Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer. BMC Genomics, 11, 352.
    • (2010) BMC Genomics , vol.11 , pp. 352
    • Pio, R.1    Blanco, D.2    Pajares, M.J.3    Aibar, E.4    Durany, O.5    Ezponda, T.6    Agorreta, J.7    Gomez-Roman, J.8    Anton, M.A.9    Rubio, A.10
  • 42
  • 43
    • 84898016349 scopus 로고    scopus 로고
    • CMGRN: A web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data
    • Guan, D., Shao, J., Deng, Y., Wang, P., Zhao, Z., Liang, Y., Wang, J. and Yan, B. (2014) CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data. Bioinformatics, 30, 1190-1192.
    • (2014) Bioinformatics , vol.30 , pp. 1190-1192
    • Guan, D.1    Shao, J.2    Deng, Y.3    Wang, P.4    Zhao, Z.5    Liang, Y.6    Wang, J.7    Yan, B.8
  • 44
    • 79959930131 scopus 로고    scopus 로고
    • ChIP-Array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
    • Qin, J., Li, M.J., Wang, P., Zhang, M.Q. and Wang, J. (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res., 39, W430-W436.
    • (2011) Nucleic Acids Res , vol.39 , pp. W430-W436
    • Qin, J.1    Li, M.J.2    Wang, P.3    Zhang, M.Q.4    Wang, J.5
  • 45
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li, B. and Dewey, C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics, 12, 323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2


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