메뉴 건너뛰기




Volumn 42, Issue 3, 2014, Pages

Interaction-based discovery of functionally important genes in cancers

Author keywords

[No Author keywords available]

Indexed keywords

DICER; F BOX PROTEIN; FBXW11 PROTEIN; METHYL CPG BINDING PROTEIN; NUCLEIC ACID; PEPTIDE; PROTEIN KINASE B; UNCLASSIFIED DRUG;

EID: 84896739938     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1305     Document Type: Article
Times cited : (26)

References (67)
  • 3
    • 84868320535 scopus 로고    scopus 로고
    • Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer
    • Liang, H., Cheung, L.W., Li, J., Ju, Z., Yu, S., Stemke-Hale, K., Dogruluk, T., Lu, Y., Liu, X., Gu, C. et al. (2012) Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer. Genome Res., 22, 2120-2129.
    • (2012) Genome Res , vol.22 , pp. 2120-2129
    • Liang, H.1    Cheung, L.W.2    Li, J.3    Ju, Z.4    Yu, S.5    Stemke-Hale, K.6    Dogruluk, T.7    Lu, Y.8    Liu, X.9    Gu, C.10
  • 4
    • 79951472909 scopus 로고    scopus 로고
    • Charting a course for genomic medicine from base pairs to bedside
    • Green, E.D. and Guyer, M.S. (2011) Charting a course for genomic medicine from base pairs to bedside. Nature, 470, 204-213.
    • (2011) Nature , vol.470 , pp. 204-213
    • Green, E.D.1    Guyer, M.S.2
  • 5
    • 84875758730 scopus 로고    scopus 로고
    • Lessons from the cancer genome
    • Garraway, L.A. and Lander, E.S. (2013) Lessons from the cancer genome. Cell, 153, 17-37.
    • (2013) Cell , vol.153 , pp. 17-37
    • Garraway, L.A.1    Lander, E.S.2
  • 12
    • 74549134502 scopus 로고    scopus 로고
    • Human cancer protein-protein interaction network: A structural perspective
    • Kar, G., Gursoy, A. and Keskin, O. (2009) Human cancer protein-protein interaction network: a structural perspective. PLoS Comput. Biol., 5, e1000601.
    • (2009) PLoS Comput. Biol , vol.5
    • Kar, G.1    Gursoy, A.2    Keskin, O.3
  • 14
    • 79955907500 scopus 로고    scopus 로고
    • The structural impact of cancer-Associated missense mutations in oncogenes and tumor suppressors
    • Stehr, H., Jang, S.H., Duarte, J.M., Wierling, C., Lehrach, H., Lappe, M. and Lange, B.M. (2011) The structural impact of cancer-Associated missense mutations in oncogenes and tumor suppressors. Mol. Cancer, 10, 54.
    • (2011) Mol. Cancer , vol.10 , pp. 54
    • Stehr, H.1    Jang, S.H.2    Duarte, J.M.3    Wierling, C.4    Lehrach, H.5    Lappe, M.6    Lange, B.M.7
  • 18
    • 78651439545 scopus 로고    scopus 로고
    • Identifying cancer driver genes in tumor genome sequencing studies
    • Youn, A. and Simon, R. (2011) Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics, 27, 175-181.
    • (2011) Bioinformatics , vol.27 , pp. 175-181
    • Youn, A.1    Simon, R.2
  • 20
    • 69249115697 scopus 로고    scopus 로고
    • Cancer-specific high-throughput annotation of somatic mutations: Computational prediction of driver missense mutations
    • Carter, H., Chen, S., Isik, L., Tyekucheva, S., Velculescu, V.E., Kinzler, K.W., Vogelstein, B. and Karchin, R. (2009) Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res., 69, 6660-6667.
    • (2009) Cancer Res , vol.69 , pp. 6660-6667
    • Carter, H.1    Chen, S.2    Isik, L.3    Tyekucheva, S.4    Velculescu, V.E.5    Kinzler, K.W.6    Vogelstein, B.7    Karchin, R.8
  • 21
    • 80053297561 scopus 로고    scopus 로고
    • A new disease-specific machine learning approach for the prediction of cancer-causing missense variants
    • Capriotti, E. and Altman, R.B. (2011) A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Genomics, 98, 310-317.
    • (2011) Genomics , vol.98 , pp. 310-317
    • Capriotti, E.1    Altman, R.B.2
  • 22
    • 84878880551 scopus 로고    scopus 로고
    • Predicting the functional consequences of cancer-Associated amino acid substitutions
    • Shihab, H.A., Gough, J., Cooper, D.N., Day, I.N. and Gaunt, T.R. (2013) Predicting the functional consequences of cancer-Associated amino acid substitutions. Bioinformatics, 29, 1504-1510.
    • (2013) Bioinformatics , vol.29 , pp. 1504-1510
    • Shihab, H.A.1    Gough, J.2    Cooper, D.N.3    Day, I.N.4    Gaunt, T.R.5
  • 23
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: Predicting amino acid changes that affect protein function
    • Ng, P.C. and Henikoff, S. (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res., 31, 3812-3814.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 24
    • 19544392545 scopus 로고    scopus 로고
    • Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information
    • Bao, L. and Cui, Y. (2005) Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information. Bioinformatics, 21, 2185-2190.
    • (2005) Bioinformatics , vol.21 , pp. 2185-2190
    • Bao, L.1    Cui, Y.2
  • 25
    • 20844461337 scopus 로고    scopus 로고
    • LS-SNP: Large-scale annotation of coding non-synonymous SNPs based on multiple information sources
    • Karchin, R., Diekhans, M., Kelly, L., Thomas, D.J., Pieper, U., Eswar, N., Haussler, D. and Sali, A. (2005) LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics, 21, 2814-2820.
    • (2005) Bioinformatics , vol.21 , pp. 2814-2820
    • Karchin, R.1    Diekhans, M.2    Kelly, L.3    Thomas, D.J.4    Pieper, U.5    Eswar, N.6    Haussler, D.7    Sali, A.8
  • 26
    • 32044453591 scopus 로고    scopus 로고
    • Identification and analysis of deleterious human SNPs
    • Yue, P. and Moult, J. (2006) Identification and analysis of deleterious human SNPs. J. Mol. Biol., 356, 1263-1274.
    • (2006) J. Mol. Biol , vol.356 , pp. 1263-1274
    • Yue, P.1    Moult, J.2
  • 29
    • 84860389647 scopus 로고    scopus 로고
    • Rare, evolutionarily unlikely missense substitutions in CHEK2 contribute to breast cancer susceptibility: Results from a breast cancer family registry case-control mutation-screening study
    • Le Calvez-Kelm, F., Lesueur, F., Damiola, F., Vallee, M., Voegele, C., Babikyan, D., Durand, G., Forey, N., McKay-Chopin, S., Robinot, N. et al. (2011) Rare, evolutionarily unlikely missense substitutions in CHEK2 contribute to breast cancer susceptibility: results from a breast cancer family registry case-control mutation-screening study. Breast Cancer Res., 13, R6.
    • (2011) Breast Cancer Res , vol.13
    • Le Calvez-Kelm, F.1    Lesueur, F.2    Damiola, F.3    Vallee, M.4    Voegele, C.5    Babikyan, D.6    Durand, G.7    Forey, N.8    McKay-Chopin, S.9    Robinot, N.10
  • 30
    • 80053189298 scopus 로고    scopus 로고
    • Predicting the functional impact of protein mutations: Application to cancer genomics
    • Reva, B., Antipin, Y. and Sander, C. (2011) Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res., 39, e118.
    • (2011) Nucleic Acids Res , vol.39
    • Reva, B.1    Antipin, Y.2    Sander, C.3
  • 31
    • 84869873569 scopus 로고    scopus 로고
    • Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation
    • Gonzalez-Perez, A., Deu-Pons, J. and Lopez-Bigas, N. (2012) Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. Genome Med., 4, 89.
    • (2012) Genome Med , vol.4 , pp. 89
    • Gonzalez-Perez, A.1    Deu-Pons, J.2    Lopez-Bigas, N.3
  • 32
    • 33748706765 scopus 로고    scopus 로고
    • Global topological features of cancer proteins in the human interactome
    • Jonsson, P.F. and Bates, P.A. (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics, 22, 2291-2297.
    • (2006) Bioinformatics , vol.22 , pp. 2291-2297
    • Jonsson, P.F.1    Bates, P.A.2
  • 34
    • 84872187316 scopus 로고    scopus 로고
    • Disentangling function from topology to infer the network properties of disease genes
    • Ghersi, D. and Singh, M. (2013) Disentangling function from topology to infer the network properties of disease genes. BMC Syst. Biol., 7, 5.
    • (2013) BMC Syst. Biol , vol.7 , pp. 5
    • Ghersi, D.1    Singh, M.2
  • 36
    • 84873802661 scopus 로고    scopus 로고
    • Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers
    • Reimand, J. and Bader, G.D. (2013) Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. Mol. Syst. Biol., 9, 637.
    • (2013) Mol. Syst. Biol , vol.9 , pp. 637
    • Reimand, J.1    Bader, G.D.2
  • 37
    • 84868010133 scopus 로고    scopus 로고
    • Domain landscapes of somatic mutations in cancer
    • Nehrt, N.L., Peterson, T.A., Park, D. and Kann, M.G. (2012) Domain landscapes of somatic mutations in cancer. BMC Genomics, 13(Suppl. 4), S9.
    • (2012) BMC Genomics , vol.13 , Issue.SUPPL. 4
    • Nehrt, N.L.1    Peterson, T.A.2    Park, D.3    Kann, M.G.4
  • 38
    • 78751584760 scopus 로고    scopus 로고
    • IWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions
    • Hosur, R., Xu, J., Bienkowska, J. and Berger, B. (2011) iWRAP: an interface threading approach with application to prediction of cancer-related protein-protein interactions. J. Mol. Biol., 405, 1295-1310.
    • (2011) J. Mol. Biol , vol.405 , pp. 1295-1310
    • Hosur, R.1    Xu, J.2    Bienkowska, J.3    Berger, B.4
  • 39
    • 84884923930 scopus 로고    scopus 로고
    • Dissecting cancer heterogeneity with a probabilistic genotype-phenotype model
    • Cho, D.Y. and Przytycka, T.M. (2013) Dissecting cancer heterogeneity with a probabilistic genotype-phenotype model. Nucleic Acids Res., 41, 8011-8020.
    • (2013) Nucleic Acids Res , vol.41 , pp. 8011-8020
    • Cho, D.Y.1    Przytycka, T.M.2
  • 40
    • 84862209073 scopus 로고    scopus 로고
    • Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases
    • Liu, Y., Koyuturk, M., Barnholtz-Sloan, J.S. and Chance, M.R. (2012) Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases. BMC Syst. Biol., 6, 65.
    • (2012) BMC Syst. Biol , vol.6 , pp. 65
    • Liu, Y.1    Koyuturk, M.2    Barnholtz-Sloan, J.S.3    Chance, M.R.4
  • 42
    • 84856532705 scopus 로고    scopus 로고
    • De novo discovery of mutated driver pathways in cancer
    • Vandin, F., Upfal, E. and Raphael, B.J. (2012) De novo discovery of mutated driver pathways in cancer. Genome Res., 22, 375-385.
    • (2012) Genome Res , vol.22 , pp. 375-385
    • Vandin, F.1    Upfal, E.2    Raphael, B.J.3
  • 45
    • 84876574278 scopus 로고    scopus 로고
    • BioLiP: A semi-manually curated database for biologically relevant ligand-protein interactions
    • Yang, J., Roy, A. and Zhang, Y. (2013) BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Res., 41, D1096-D1103.
    • (2013) Nucleic Acids Res , vol.41
    • Yang, J.1    Roy, A.2    Zhang, Y.3
  • 48
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Methodol., 57, 289-300.
    • (1995) J. R. Stat. Soc. B Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 49
    • 27744606052 scopus 로고    scopus 로고
    • The importance of immune gene variability (MHC) in evolutionary ecology and conservation
    • Sommer, S. (2005) The importance of immune gene variability (MHC) in evolutionary ecology and conservation. Front. Zool., 2, 16.
    • (2005) Front. Zool , vol.2 , pp. 16
    • Sommer, S.1
  • 52
    • 35348983404 scopus 로고    scopus 로고
    • Homodimeric structure and double-stranded RNA cleavage activity of the C-terminal RNase III domain of human dicer
    • Takeshita, D., Zenno, S., Lee, W.C., Nagata, K., Saigo, K. and Tanokura, M. (2007) Homodimeric structure and double-stranded RNA cleavage activity of the C-terminal RNase III domain of human dicer. J. Mol. Biol., 374, 106-120.
    • (2007) J. Mol. Biol , vol.374 , pp. 106-120
    • Takeshita, D.1    Zenno, S.2    Lee, W.C.3    Nagata, K.4    Saigo, K.5    Tanokura, M.6
  • 54
    • 0037162293 scopus 로고    scopus 로고
    • High-resolution structure of the pleckstrin homology domain of protein kinase b/akt bound to phosphatidylinositol (3,4, 5)-trisphosphate
    • Thomas, C.C., Deak, M., Alessi, D.R. and van Aalten, D.M. (2002) High-resolution structure of the pleckstrin homology domain of protein kinase b/akt bound to phosphatidylinositol (3, 4, 5)-trisphosphate. Curr. Biol., 12, 1256-1262.
    • (2002) Curr. Biol , vol.12 , pp. 1256-1262
    • Thomas, C.C.1    Deak, M.2    Alessi, D.R.3    Van Aalten, D.M.4
  • 55
    • 0035906936 scopus 로고    scopus 로고
    • Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA
    • Ohki, I., Shimotake, N., Fujita, N., Jee, J., Ikegami, T., Nakao, M. and Shirakawa, M. (2001) Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA. Cell, 105, 487-497.
    • (2001) Cell , vol.105 , pp. 487-497
    • Ohki, I.1    Shimotake, N.2    Fujita, N.3    Jee, J.4    Ikegami, T.5    Nakao, M.6    Shirakawa, M.7
  • 56
    • 0037756787 scopus 로고    scopus 로고
    • Structure of a beta-TrCP1-Skp1-beta-catenin complex: Destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase
    • Wu, G., Xu, G., Schulman, B.A., Jeffrey, P.D., Harper, J.W. and Pavletich, N.P. (2003) Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase. Mol. Cell, 11, 1445-1456.
    • (2003) Mol. Cell , vol.11 , pp. 1445-1456
    • Wu, G.1    Xu, G.2    Schulman, B.A.3    Jeffrey, P.D.4    Harper, J.W.5    Pavletich, N.P.6
  • 57
    • 34247593034 scopus 로고    scopus 로고
    • Impaired microRNA processing enhances cellular transformation and tumorigenesis
    • Kumar, M.S., Lu, J., Mercer, K.L., Golub, T.R. and Jacks, T. (2007) Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat. Genet., 39, 673-677.
    • (2007) Nat. Genet , vol.39 , pp. 673-677
    • Kumar, M.S.1    Lu, J.2    Mercer, K.L.3    Golub, T.R.4    Jacks, T.5
  • 59
    • 84872958116 scopus 로고    scopus 로고
    • Cancer-Associated somatic DICER1 hotspot mutations cause defective miRNA processing and reverse-strand expression bias to predominantly mature 3p strands through loss of 5p strand cleavage
    • Anglesio, M.S., Wang, Y., Yang, W., Senz, J., Wan, A., Heravi-Moussavi, A., Salamanca, C., Maines-Bandiera, S., Huntsman, D.G. and Morin, G.B. (2013) Cancer-Associated somatic DICER1 hotspot mutations cause defective miRNA processing and reverse-strand expression bias to predominantly mature 3p strands through loss of 5p strand cleavage. J. Pathol., 229, 400-409.
    • (2013) J. Pathol , vol.229 , pp. 400-409
    • Anglesio, M.S.1    Wang, Y.2    Yang, W.3    Senz, J.4    Wan, A.5    Heravi-Moussavi, A.6    Salamanca, C.7    Maines-Bandiera, S.8    Huntsman, D.G.9    Morin, G.B.10
  • 60
    • 77749292082 scopus 로고    scopus 로고
    • The Akt isoforms are present at distinct subcellular locations
    • Santi, S.A. and Lee, H. (2010) The Akt isoforms are present at distinct subcellular locations. Am. J .Physiol. Cell Physiol., 298, C580-C591.
    • (2010) Am J .Physiol. Cell Physiol , vol.298
    • Santi, S.A.1    Lee, H.2
  • 63
    • 78349233845 scopus 로고    scopus 로고
    • Rarity of AKT1 and AKT3 E17K mutations in squamous cell carcinoma of lung
    • Do, H., Salemi, R., Murone, C., Mitchell, P.L. and Dobrovic, A. (2010) Rarity of AKT1 and AKT3 E17K mutations in squamous cell carcinoma of lung. Cell Cycle, 9, 4411-4412.
    • (2010) Cell Cycle , vol.9 , pp. 4411-4412
    • Do, H.1    Salemi, R.2    Murone, C.3    Mitchell, P.L.4    Dobrovic, A.5
  • 64
    • 0032772371 scopus 로고    scopus 로고
    • Methylation-mediated transcriptional silencing in euchromatin by methyl-CpG binding protein MBD1 isoforms
    • Fujita, N., Takebayashi, S., Okumura, K., Kudo, S., Chiba, T., Saya, H. and Nakao, M. (1999) Methylation-mediated transcriptional silencing in euchromatin by methyl-CpG binding protein MBD1 isoforms. Mol. Cell. Biol., 19, 6415-6426.
    • (1999) Mol. Cell. Biol , vol.19 , pp. 6415-6426
    • Fujita, N.1    Takebayashi, S.2    Okumura, K.3    Kudo, S.4    Chiba, T.5    Saya, H.6    Nakao, M.7
  • 65
    • 0033602475 scopus 로고    scopus 로고
    • HOS, a human homolog of Slimb, forms an SCF complex with Skp1 and Cullin1 and targets the phosphorylation-dependent degradation of IkappaB and beta-catenin
    • Fuchs, S.Y., Chen, A., Xiong, Y., Pan, Z.Q. and Ronai, Z. (1999) HOS, a human homolog of Slimb, forms an SCF complex with Skp1 and Cullin1 and targets the phosphorylation-dependent degradation of IkappaB and beta-catenin. Oncogene, 18, 2039-2046.
    • (1999) Oncogene , vol.18 , pp. 2039-2046
    • Fuchs, S.Y.1    Chen, A.2    Xiong, Y.3    Pan, Z.Q.4    Ronai, Z.5
  • 66
    • 0033486152 scopus 로고    scopus 로고
    • Beta-catenin signaling and cancer
    • Morin, P.J. (1999) beta-catenin signaling and cancer. Bioessays, 21, 1021-1030.
    • (1999) Bioessays , vol.21 , pp. 1021-1030
    • Morin, P.J.1
  • 67
    • 0033895709 scopus 로고    scopus 로고
    • Wnt signaling and cancer
    • Polakis, P. (2000) Wnt signaling and cancer. Genes Dev., 14, 1837-1851.
    • (2000) Genes Dev , vol.14 , pp. 1837-1851
    • Polakis, P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.