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Volumn 23, Issue 4, 2013, Pages 213-218

Integrated network analyses for functional genomic studies in cancer

Author keywords

Computational modeling; Regulatory networks; RNAi; Signaling pathways

Indexed keywords

ACUTE LYMPHOBLASTIC LEUKEMIA; BREAST CANCER; CANCER GENETICS; CANCER GROWTH; CANCER RESISTANCE; CARCINOGENESIS; COMPUTER MODEL; COMPUTER NETWORK; COPY NUMBER VARIATION; FUNCTIONAL GENOMICS; GENE REGULATORY NETWORK; GENE TARGETING; GENETIC ENGINEERING; GENETIC SCREENING; GENETIC VARIABILITY; GLIOBLASTOMA; HIGH THROUGHPUT SCREENING; HUMAN; MALIGNANT NEOPLASTIC DISEASE; MOLECULAR INTERACTION; NONHUMAN; REVIEW; RNA INTERFERENCE; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 84881104520     PISSN: 1044579X     EISSN: 10963650     Source Type: Journal    
DOI: 10.1016/j.semcancer.2013.06.004     Document Type: Review
Times cited : (14)

References (32)
  • 1
  • 3
    • 84875485693 scopus 로고    scopus 로고
    • Cancer pharmacogenomics: early promise, but concerted effort needed
    • McLeod H.L. Cancer pharmacogenomics: early promise, but concerted effort needed. Science 2013, 339(6127):1563-1566.
    • (2013) Science , vol.339 , Issue.6127 , pp. 1563-1566
    • McLeod, H.L.1
  • 4
    • 84876576325 scopus 로고    scopus 로고
    • Computational solutions for omics data
    • Berger B., Peng J., Singh M. Computational solutions for omics data. Nat Rev Genet 2013, 14(5):333-346.
    • (2013) Nat Rev Genet , vol.14 , Issue.5 , pp. 333-346
    • Berger, B.1    Peng, J.2    Singh, M.3
  • 6
    • 77953626646 scopus 로고    scopus 로고
    • Genomic screening with RNAi: results and challenges
    • Mohr S., Bakal C., Perrimon N. Genomic screening with RNAi: results and challenges. Annu Rev Biochem 2010, 79(1):37-64.
    • (2010) Annu Rev Biochem , vol.79 , Issue.1 , pp. 37-64
    • Mohr, S.1    Bakal, C.2    Perrimon, N.3
  • 7
    • 84864326893 scopus 로고    scopus 로고
    • Use and abuse of RNAi to study mammalian gene function
    • Kaelin W.G., Molecular biology. Use and abuse of RNAi to study mammalian gene function. Science 2012, 337(6093):421-422.
    • (2012) Science , vol.337 , Issue.6093 , pp. 421-422
    • Kaelin, W.G.1    Molecular, B.2
  • 8
    • 79952674000 scopus 로고    scopus 로고
    • Interactome networks and human disease
    • Vidal M., Cusick M.E., Barabási A.-L. Interactome networks and human disease. Cell 2011, 144(6):986-998.
    • (2011) Cell , vol.144 , Issue.6 , pp. 986-998
    • Vidal, M.1    Cusick, M.E.2    Barabási, A.-L.3
  • 9
    • 79251469386 scopus 로고    scopus 로고
    • Vigilance and validation: keys to success in RNAi screening
    • Sigoillot F.D., King R.W. Vigilance and validation: keys to success in RNAi screening. ACS Chem Biol 2011, 6(1):47-60.
    • (2011) ACS Chem Biol , vol.6 , Issue.1 , pp. 47-60
    • Sigoillot, F.D.1    King, R.W.2
  • 11
    • 74049124186 scopus 로고    scopus 로고
    • Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application
    • Jackson A.L., Linsley P.S. Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application. Nat Rev Drug Discov 2010, 9(57):1-11.
    • (2010) Nat Rev Drug Discov , vol.9 , Issue.57 , pp. 1-11
    • Jackson, A.L.1    Linsley, P.S.2
  • 12
    • 84857781943 scopus 로고    scopus 로고
    • A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response
    • Adamson B., Smogorzewska A., Sigoillot F.D., King R.W., Elledge S.J. A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nat Cell Biol 2012, 14(3):318-328.
    • (2012) Nat Cell Biol , vol.14 , Issue.3 , pp. 318-328
    • Adamson, B.1    Smogorzewska, A.2    Sigoillot, F.D.3    King, R.W.4    Elledge, S.J.5
  • 13
    • 56349121125 scopus 로고    scopus 로고
    • An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer
    • Zender L., Xue W., Zuber J., Semighini C.P., Krasnitz A., Ma B., et al. An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell 2008, 135(5):852-864.
    • (2008) Cell , vol.135 , Issue.5 , pp. 852-864
    • Zender, L.1    Xue, W.2    Zuber, J.3    Semighini, C.P.4    Krasnitz, A.5    Ma, B.6
  • 14
    • 84859218649 scopus 로고    scopus 로고
    • A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens
    • Sigoillot F.D., Lyman S., Huckins J.F., Adamson B., Chung E., Quattrochi B., et al. A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nature Methods 2012, 9(4):363-366.
    • (2012) Nature Methods , vol.9 , Issue.4 , pp. 363-366
    • Sigoillot, F.D.1    Lyman, S.2    Huckins, J.F.3    Adamson, B.4    Chung, E.5    Quattrochi, B.6
  • 15
    • 79961062492 scopus 로고    scopus 로고
    • Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer
    • Mesirov J., Garraway L. Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. PNAS 2011, 108:12372-12377.
    • (2011) PNAS , vol.108 , pp. 12372-12377
    • Mesirov, J.1    Garraway, L.2
  • 16
    • 0037370309 scopus 로고    scopus 로고
    • An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo
    • Hemann M.T., Fridman J.S., Zilfou J.T., Hernando E., Paddison P.J., Cordon-Cardo C., et al. An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nat Genet 2003, 33(3):396-400.
    • (2003) Nat Genet , vol.33 , Issue.3 , pp. 396-400
    • Hemann, M.T.1    Fridman, J.S.2    Zilfou, J.T.3    Hernando, E.4    Paddison, P.J.5    Cordon-Cardo, C.6
  • 17
    • 34247248169 scopus 로고    scopus 로고
    • Epi-allelic Erk1 and Erk2 knockdown series for quantitative analysis of T cell Erk regulation and IL-2 production
    • Wille L., Kemp M.L., Sandy P., Lewis C.L., Lauffenburger D.A. Epi-allelic Erk1 and Erk2 knockdown series for quantitative analysis of T cell Erk regulation and IL-2 production. Mol Immunol 2007, 44(12):3085-3091.
    • (2007) Mol Immunol , vol.44 , Issue.12 , pp. 3085-3091
    • Wille, L.1    Kemp, M.L.2    Sandy, P.3    Lewis, C.L.4    Lauffenburger, D.A.5
  • 18
    • 78650373804 scopus 로고    scopus 로고
    • Network medicine: a network-based approach to human disease
    • Barabási A.-L., Gulbahce N., Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet 2011, 12(1):56-68.
    • (2011) Nat Rev Genet , vol.12 , Issue.1 , pp. 56-68
    • Barabási, A.-L.1    Gulbahce, N.2    Loscalzo, J.3
  • 19
    • 84859994220 scopus 로고    scopus 로고
    • Computational approaches for analyzing information flow in biological networks
    • Kholodenko B., Yaffe M.B., Kolch W. Computational approaches for analyzing information flow in biological networks. Sci Signal 2012, 5(220):re1.
    • (2012) Sci Signal , vol.5 , Issue.220
    • Kholodenko, B.1    Yaffe, M.B.2    Kolch, W.3
  • 20
    • 84875750487 scopus 로고    scopus 로고
    • The scientific drunk and the lamppost: massive sequencing efforts in cancer discovery and treatment
    • Yaffe M.B. The scientific drunk and the lamppost: massive sequencing efforts in cancer discovery and treatment. Sci Signal 2013, 6(269):pe13-pe23.
    • (2013) Sci Signal , vol.6 , Issue.269
    • Yaffe, M.B.1
  • 21
    • 84863011640 scopus 로고    scopus 로고
    • Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress
    • Tentner A.R., Lee M.J., Ostheimer G.J., Samson L.D., Lauffenburger D.A., Yaffe M.B. Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress. Mol Syst Biol 2012, 8:1-18.
    • (2012) Mol Syst Biol , vol.8 , pp. 1-18
    • Tentner, A.R.1    Lee, M.J.2    Ostheimer, G.J.3    Samson, L.D.4    Lauffenburger, D.A.5    Yaffe, M.B.6
  • 22
    • 84864286442 scopus 로고    scopus 로고
    • Widespread potential for growth-factor-driven resistance to anticancer kinase inhibitors
    • Wilson T.R., Fridlyand J., Yan Y., Penuel E., Burton L., Chan E., et al. Widespread potential for growth-factor-driven resistance to anticancer kinase inhibitors. Nature 2012, 487(7408):505-509.
    • (2012) Nature , vol.487 , Issue.7408 , pp. 505-509
    • Wilson, T.R.1    Fridlyand, J.2    Yan, Y.3    Penuel, E.4    Burton, L.5    Chan, E.6
  • 23
    • 84880886028 scopus 로고    scopus 로고
    • Receptor tyrosine kinases fall into distinct classes based on their inferred signaling networks
    • [in press]
    • Wagner J., Wolf-Yadlin A., Sevecka M., Grenier J., Root D., Lauffenburger D.A., et al. Receptor tyrosine kinases fall into distinct classes based on their inferred signaling networks. Sci Signal 2013, [in press].
    • (2013) Sci Signal
    • Wagner, J.1    Wolf-Yadlin, A.2    Sevecka, M.3    Grenier, J.4    Root, D.5    Lauffenburger, D.A.6
  • 25
    • 67651219232 scopus 로고    scopus 로고
    • A network of conserved damage survival pathways revealed by a genomic RNAi screen
    • Ravi D., Wiles A.M., Bhavani S., Ruan J., Leder P., Bishop A.J.R. A network of conserved damage survival pathways revealed by a genomic RNAi screen. PLoS Genet 2009, 5(6):e1000527.
    • (2009) PLoS Genet , vol.5 , Issue.6
    • Ravi, D.1    Wiles, A.M.2    Bhavani, S.3    Ruan, J.4    Leder, P.5    Bishop, A.J.R.6
  • 26
    • 52149123619 scopus 로고    scopus 로고
    • Core signaling pathways in human pancreatic cancers revealed by global genomic analyses
    • Jones S., Zhang X., Parsons D.W., Lin J.C., Leary R.J., Angenendt P., et al. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008, 321(5897):1801-1806.
    • (2008) Science , vol.321 , Issue.5897 , pp. 1801-1806
    • Jones, S.1    Zhang, X.2    Parsons, D.W.3    Lin, J.C.4    Leary, R.J.5    Angenendt, P.6
  • 27
    • 84859994220 scopus 로고    scopus 로고
    • Computational approaches for analyzing information flow in biological networks
    • Kholodenko B., Yaffe M.B., Kolch W. Computational approaches for analyzing information flow in biological networks. Sci Signal 2012, 5(220).
    • (2012) Sci Signal , vol.5 , Issue.220
    • Kholodenko, B.1    Yaffe, M.B.2    Kolch, W.3
  • 28
    • 79960888804 scopus 로고    scopus 로고
    • Inferring causal genomic alterations in breast cancer using gene expression data
    • Tran L.M., Bin Zhang, Zhang Z., Zhang C., Xie T., Lamb J., et al. Inferring causal genomic alterations in breast cancer using gene expression data. BMC Syst Biol 2011, 5(1):121.
    • (2011) BMC Syst Biol , vol.5 , Issue.1 , pp. 121
    • Tran, L.M.1    Bin Zhang2    Zhang, Z.3    Zhang, C.4    Xie, T.5    Lamb, J.6
  • 29
    • 84874766054 scopus 로고    scopus 로고
    • Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling
    • Huang S.-S.C., Clarke D.C., Gosline S.J.C., Labadorf A., Chouinard C., Gordon W., et al. Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PLoS Comput Biol 2013, 9(2):e1002887.
    • (2013) PLoS Comput Biol , vol.9 , Issue.2
    • Huang, S.-S.C.1    Clarke, D.C.2    Gosline, S.J.C.3    Labadorf, A.4    Chouinard, C.5    Gordon, W.6
  • 30
    • 84872684650 scopus 로고    scopus 로고
    • Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach
    • Lee M.N., Roy M., Ong S.-E., Mertins P., Villani A., Li W., et al. Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach. Nat Immunol 2012, 14(2):179-185.
    • (2012) Nat Immunol , vol.14 , Issue.2 , pp. 179-185
    • Lee, M.N.1    Roy, M.2    Ong, S.-E.3    Mertins, P.4    Villani, A.5    Li, W.6
  • 31
    • 40749105508 scopus 로고    scopus 로고
    • Variations in DNA elucidate molecular networks that cause disease
    • Chen Y., Zhu J., Lum P.Y., Pinto S., MacNeil D.J., Zhang C., et al. Variations in DNA elucidate molecular networks that cause disease. Nature 2008, 452(7186):429-435.
    • (2008) Nature , vol.452 , Issue.7186 , pp. 429-435
    • Chen, Y.1    Zhu, J.2    Lum, P.Y.3    Pinto, S.4    MacNeil, D.J.5    Zhang, C.6
  • 32
    • 84874419781 scopus 로고    scopus 로고
    • SAMNET: a network-based approach to integrate multi-dimensional high throughput datasets
    • Gosline S.J.C., Spencer S., Orsu O., Fraenkel E. SAMNET: a network-based approach to integrate multi-dimensional high throughput datasets. Integr Biol 2012, 4(11):1415-1427.
    • (2012) Integr Biol , vol.4 , Issue.11 , pp. 1415-1427
    • Gosline, S.J.C.1    Spencer, S.2    Orsu, O.3    Fraenkel, E.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.