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Volumn 11, Issue 7, 2010, Pages 721-734

Taking a systems approach to the identification of novel therapeutic targets and biomarkers

Author keywords

Chemical biology; High content screening; Multivariate analysis; Ontological classification; Predictive modeling; Proteomics; Transcriptomics

Indexed keywords

BIOLOGICAL MARKER;

EID: 78649300684     PISSN: 13892010     EISSN: 18734316     Source Type: Journal    
DOI: 10.2174/138920110792927739     Document Type: Article
Times cited : (7)

References (141)
  • 1
    • 0037441560 scopus 로고    scopus 로고
    • Fulfilling the promise: Drug discovery in the post-genomic era
    • Chanda, S.; Caldwell, J. Fulfilling the promise: drug discovery in the post-genomic era. Drug Discov. Today, 2003, 8(4), 168-174.
    • (2003) Drug Discov. Today , vol.8 , Issue.4 , pp. 168-174
    • Chanda, S.1    Caldwell, J.2
  • 2
    • 46349109932 scopus 로고    scopus 로고
    • Systems biology: An evolving approach in drug discovery and development
    • Ho, R.L.; Lieu, C.A. Systems biology: an evolving approach in drug discovery and development. Drugs R. D., 2008, 9(4), 203-216.
    • (2008) Drugs R. D , vol.9 , Issue.4 , pp. 203-216
    • Ho, R.L.1    Lieu, C.A.2
  • 3
    • 72949101438 scopus 로고    scopus 로고
    • Structure and organization of drug-target networks: Insights from genomic approaches for drug discovery. Mol. Biol
    • Janga, S.C.; Tzakos, A. Structure and organization of drug-target networks: insights from genomic approaches for drug discovery. Mol. Biol. Syst., 2009, 5, 1536-1548.
    • (2009) Syst , vol.5 , pp. 1536-1548
    • Janga, S.C.1    Tzakos, A.2
  • 4
    • 25644454404 scopus 로고    scopus 로고
    • Pharmaceuticals: A new grammar for drug discovery
    • Fishman, M.C.; Porter, J.A. Pharmaceuticals: a new grammar for drug discovery. Nature, 2005, 437, 491-493.
    • (2005) Nature , vol.437 , pp. 491-493
    • Fishman, M.C.1    Porter, J.A.2
  • 6
    • 5044229321 scopus 로고    scopus 로고
    • The impact of systems approaches on biological problems in drug discovery
    • Hood, L.; Perlmutter, R.M. The impact of systems approaches on biological problems in drug discovery. Nat. Biotechnol., 2004, 22, 1215-1217.
    • (2004) Nat. Biotechnol , vol.22 , pp. 1215-1217
    • Hood, L.1    Perlmutter, R.M.2
  • 7
    • 20844432908 scopus 로고    scopus 로고
    • Can cell systems biology rescue drug discovery?
    • Butcher, E.C. Can cell systems biology rescue drug discovery? Nat. Rev. Drug Discov., 2005, 4(6), 461-467.
    • (2005) Nat. Rev. Drug Discov , vol.4 , Issue.6 , pp. 461-467
    • Butcher, E.C.1
  • 8
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: The next paradigm in drug discovery
    • Hopkins, A.L. Network pharmacology: the next paradigm in drug discovery. Nat. Chem. Biol., 2008, 4(11), 682-690.
    • (2008) Nat. Chem. Biol , vol.4 , Issue.11 , pp. 682-690
    • Hopkins, A.L.1
  • 9
    • 70449522311 scopus 로고    scopus 로고
    • Towards a systems biology approach of G protein-coupled receptor signaling: Challenges and expectations
    • Heitzler, D.; Crépieux, P.; Poupon, A.; Clément, F.; Fages, F.; Reiter, E. Towards a systems biology approach of G protein-coupled receptor signaling: challenges and expectations. C. R. Biol., 2009, 332(11), 947-957.
    • (2009) C. R. Biol , vol.332 , Issue.11 , pp. 947-957
    • Heitzler, D.1    Crépieux, P.2    Poupon, A.3    Clément, F.4    Fages, F.5    Reiter, E.6
  • 11
    • 65649087098 scopus 로고    scopus 로고
    • Breast cancer: Understanding sensitivity and resistance to chemotherapy and targeted therapies to aid in personalised medicine
    • Germano, S.; O'Driscoll, L. Breast cancer: understanding sensitivity and resistance to chemotherapy and targeted therapies to aid in personalised medicine. Curr. Cancer Drug Targets, 2009, 9(3), 398-418.
    • (2009) Curr. Cancer Drug Targets , vol.9 , Issue.3 , pp. 398-418
    • Germano, S.1    O'Driscoll, L.2
  • 13
    • 5044226336 scopus 로고    scopus 로고
    • Systems biology in drug discovery
    • Butcher, E. C.; Berg, E. L.; Kunkel, E. J. Systems biology in drug discovery. Nat. Biotechnol., 2004, 22(10),1253-1259.
    • (2004) Nat. Biotechnol , vol.22 , Issue.10 , pp. 1253-1259
    • Butcher, E.C.1    Berg, E.L.2    Kunkel, E.J.3
  • 15
    • 40749153465 scopus 로고    scopus 로고
    • A systems biology approach to drug discovery
    • Zhu, J.; Zhang, B.; Schadt, E.E. A systems biology approach to drug discovery. Adv. Genet., 2008, 60, 603-635.
    • (2008) Adv. Genet , vol.60 , pp. 603-635
    • Zhu, J.1    Zhang, B.2    Schadt, E.E.3
  • 16
    • 33745960413 scopus 로고    scopus 로고
    • Proteomics technology in systems biology
    • Smith, J.C.; Figeys, D.; Proteomics technology in systems biology. Mol. Biosyst., 2006, 2(8), 364-370.
    • (2006) Mol. Biosyst , vol.2 , Issue.8 , pp. 364-370
    • Smith, J.C.1    Figeys, D.2
  • 18
    • 30544454201 scopus 로고    scopus 로고
    • Metabolomics reviewed: A new omics platform technology for systems biology and implications for natural products research
    • Rochfort, S. Metabolomics reviewed: a new omics platform technology for systems biology and implications for natural products research. J. Nat. Prod., 2005, 68(12), 1813-1820.
    • (2005) J. Nat. Prod , vol.68 , Issue.12 , pp. 1813-1820
    • Rochfort, S.1
  • 19
    • 0142040405 scopus 로고    scopus 로고
    • Metabolomics in systems biology
    • Weckwerth, W. Metabolomics in systems biology. Annu. Rev. Plant Biol., 2003, 54, 669-689.
    • (2003) Annu. Rev. Plant Biol , vol.54 , pp. 669-689
    • Weckwerth, W.1
  • 20
    • 34250638746 scopus 로고    scopus 로고
    • F. siRNAs in drug discovery: Target validation and beyond
    • Natt
    • Natt, F. siRNAs in drug discovery: target validation and beyond. Curr. Opin. Mol. Ther., 2007, 9(3), 242-247.
    • (2007) Curr. Opin. Mol. Ther , vol.9 , Issue.3 , pp. 242-247
  • 21
    • 19944430064 scopus 로고    scopus 로고
    • High-throughput RNA interference strategies for target discovery and validation by using synthetic short-interfering RNAs: Functional genomics investigations of biological pathways
    • Sachse, C.; Krausz, E.; Krönke, A.; Hannus, M.; Walsh, A.; Grabner, A.; Ovcharenko, D.; Dorris, D.; Trudel, C.; Sönnichsen, B.; Echeverri, C.J. High-throughput RNA interference strategies for target discovery and validation by using synthetic short-interfering RNAs: functional genomics investigations of biological pathways. Methods Enzymol., 2005, 392, 242-277.
    • (2005) Methods Enzymol , vol.392 , pp. 242-277
    • Sachse, C.1    Krausz, E.2    Krönke, A.3    Hannus, M.4    Walsh, A.5    Grabner, A.6    Ovcharenko, D.7    Dorris, D.8    Trudel, C.9    Sönnichsen, B.10    Echeverri, C.J.11
  • 22
    • 33747624926 scopus 로고    scopus 로고
    • High-throughput fluorescence micros-copy for systems biology
    • Pepperkok, R.; Ellenberg, J. High-throughput fluorescence micros-copy for systems biology. Nat. Rev. Mol. Cell Biol., 2006, 7(9), 690-696.
    • (2006) Nat. Rev. Mol. Cell Biol , vol.7 , Issue.9 , pp. 690-696
    • Pepperkok, R.1    Ellenberg, J.2
  • 24
    • 12344288635 scopus 로고    scopus 로고
    • Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets
    • Eggert, U.S.; Kiger, A.A.; Richter, C.; Perlman, Z.E.; Perrimon, N.; Mitchison, T.J.; Field, C.M. Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets. PLoS Biol., 2004, 2(12), 2135-2143.
    • (2004) PLoS Biol , vol.2 , Issue.12 , pp. 2135-2143
    • Eggert, U.S.1    Kiger, A.A.2    Richter, C.3    Perlman, Z.E.4    Perrimon, N.5    Mitchison, T.J.6    Field, C.M.7
  • 25
    • 34249986315 scopus 로고    scopus 로고
    • Chemogenomics approaches to novel target discovery
    • Gaither, L.A. Chemogenomics approaches to novel target discovery. Expert Rev. Proteomics, 2007, 4(3), 411-419.
    • (2007) Expert Rev. Proteomics , vol.4 , Issue.3 , pp. 411-419
    • Gaither, L.A.1
  • 29
    • 31144432293 scopus 로고    scopus 로고
    • Literature mining for the biologist: From information retrieval to biological discovery
    • Jensen, L.J.; Saric, J.; Bork P. Literature mining for the biologist: from information retrieval to biological discovery. Nat. Rev. Genet., 2006, 7(2),119-129.
    • (2006) Nat. Rev. Genet , vol.7 , Issue.2 , pp. 119-129
    • Jensen, L.J.1    Saric, J.2    Bork, P.3
  • 31
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Kanehisa, M.; Goto, S.; Furumichi, M.; Tanabe, M.; Hirakawa, M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 2010, 38 (Database issue), D355-360.
    • (2010) Nucleic Acids Res , vol.38 , Issue.Database issue
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3    Tanabe, M.4    Hirakawa, M.5
  • 32
    • 35348858911 scopus 로고    scopus 로고
    • Cell-based high-content screening of small-molecule libraries
    • Korn, K.; Krausz, E. Cell-based high-content screening of small-molecule libraries. Curr. Opin. Chem. Biol., 2007, 11 (5), 503-510
    • (2007) Curr. Opin. Chem. Biol , vol.11 , Issue.5 , pp. 503-510
    • Korn, K.1    Krausz, E.2
  • 34
    • 70349449748 scopus 로고    scopus 로고
    • Applications of high content screening in life science research. Comb
    • Zock, J.M. Applications of high content screening in life science research. Comb. Chem. High Throughput. Screen, 2009, 12(9), 870-876.
    • (2009) Chem. High Throughput. Screen , vol.12 , Issue.9 , pp. 870-876
    • Zock, J.M.1
  • 35
    • 34447502161 scopus 로고    scopus 로고
    • Image-based chemical screening
    • Carpenter, A.E. Image-based chemical screening. Nat. Chem. Biol., 2007, 3(8), 461-465.
    • (2007) Nat. Chem. Biol , vol.3 , Issue.8 , pp. 461-465
    • Carpenter, A.E.1
  • 39
    • 33750803554 scopus 로고    scopus 로고
    • An infrastructure for high-throughput microscopy: Instrumentation, informatics, and integration
    • Vaisberg, E.A.; Lenzi, D.; Hansen, R.L.; Keon, B.H.; Finer, J.T. An infrastructure for high-throughput microscopy: instrumentation, informatics, and integration. Methods Enzymol., 2006, 414, 484-512.
    • (2006) Methods Enzymol , vol.414 , pp. 484-512
    • Vaisberg, E.A.1    Lenzi, D.2    Hansen, R.L.3    Keon, B.H.4    Finer, J.T.5
  • 40
    • 14844336297 scopus 로고    scopus 로고
    • Biomaterial microarrays: Rapid, microscale screening of polymer-cell interaction
    • Anderson, D.G.; Putnam, D.; Lavik, E.B.; Mahmood, T.A.; Langer, R. Biomaterial microarrays: rapid, microscale screening of polymer-cell interaction. Biomaterials, 2005, 26(23), 4892-4897.
    • (2005) Biomaterials , vol.26 , Issue.23 , pp. 4892-4897
    • Anderson, D.G.1    Putnam, D.2    Lavik, E.B.3    Mahmood, T.A.4    Langer, R.5
  • 43
    • 33747152561 scopus 로고    scopus 로고
    • Matrix elasticity directs stem cell lineage specification
    • Engler, A.J.; Sen, S.; Sweeney, H.L.; Discher, D.E. Matrix elasticity directs stem cell lineage specification. Cell, 2006, 126(4), 677-689.
    • (2006) Cell , vol.126 , Issue.4 , pp. 677-689
    • Engler, A.J.1    Sen, S.2    Sweeney, H.L.3    Discher, D.E.4
  • 44
    • 33747154172 scopus 로고    scopus 로고
    • Matrix control of stem cell fate
    • Even-Ram, S.; Artym, V.; Yamada, K.M. Matrix control of stem cell fate. Cell, 2006, 126(4), 645-647.
    • (2006) Cell , vol.126 , Issue.4 , pp. 645-647
    • Even-Ram, S.1    Artym, V.2    Yamada, K.M.3
  • 45
    • 39049185794 scopus 로고    scopus 로고
    • Reagents to measure and manipulate cell functions
    • Giuliano, K.A.; Taylor, D.L.; Waggoner, A.S. Reagents to measure and manipulate cell functions. Methods Mol. Biol., 2007, 356, 141-163.
    • (2007) Methods Mol. Biol , vol.356 , pp. 141-163
    • Giuliano, K.A.1    Taylor, D.L.2    Waggoner, A.S.3
  • 46
    • 0346158531 scopus 로고    scopus 로고
    • High content screening applied to large-scale cell biology
    • Abraham, V.C.; Taylor, D.L.; Haskins, J.R. High content screening applied to large-scale cell biology. Trends Biotechnol., 2004, 22(1), 15-22.
    • (2004) Trends Biotechnol , vol.22 , Issue.1 , pp. 15-22
    • Abraham, V.C.1    Taylor, D.L.2    Haskins, J.R.3
  • 49
    • 0242578486 scopus 로고    scopus 로고
    • Use of green fluorescent protein (GFP) and its homologs for in vivo protein motility studies
    • Chudakov, D.M.; Lukyanov, K.A. Use of green fluorescent protein (GFP) and its homologs for in vivo protein motility studies. Biochemistry, (Mosc) 2003, 68(9), 952-957.
    • (2003) Biochemistry, (Mosc) , vol.68 , Issue.9 , pp. 952-957
    • Chudakov, D.M.1    Lukyanov, K.A.2
  • 50
    • 0037225979 scopus 로고    scopus 로고
    • Immunofluorescent labeling of cancer marker Her2 and other cellular targets with semiconductor quantum dots
    • Wu, X.; Liu, H.; Liu, J.; Haley, K.N.; Treadway, J.A.; Larson, J.P.; Ge, N.; Peale, F.; Bruchez, M.P. Immunofluorescent labeling of cancer marker Her2 and other cellular targets with semiconductor quantum dots. Nat. Biotechnol., 2003, 21(1), 41-62.
    • (2003) Nat. Biotechnol , vol.21 , Issue.1 , pp. 41-62
    • Wu, X.1    Liu, H.2    Liu, J.3    Haley, K.N.4    Treadway, J.A.5    Larson, J.P.6    Ge, N.7    Peale, F.8    Bruchez, M.P.9
  • 51
    • 0348087040 scopus 로고    scopus 로고
    • Long-term multiple color imaging of live cells using quantum dot bioconjugates
    • Jaiswal, J.K.; Mattoussi, H.; Mauro, J. M.; Simon, S.M. Long-term multiple color imaging of live cells using quantum dot bioconjugates. Nat. Biotechnol., 2003, (1), 47-51.
    • (2003) Nat. Biotechnol , Issue.1 , pp. 47-51
    • Jaiswal, J.K.1    Mattoussi, H.2    Mauro, J.M.3    Simon S.M4
  • 53
    • 0037138650 scopus 로고    scopus 로고
    • Diversity-oriented synthesis of biaryl-containing medium rings using a one bead/one stock solution platform
    • Spring, D.R.; Krishnan, S.; Blackwell, H. E.; Schreiber, S.L. Diversity-oriented synthesis of biaryl-containing medium rings using a one bead/one stock solution platform. J. Am. Chem. Soc., 2002, 124(7), 1354-1363.
    • (2002) J. Am. Chem. Soc , vol.124 , Issue.7 , pp. 1354-1363
    • Spring, D.R.1    Krishnan, S.2    Blackwell, H.E.3    Schreiber, S.L.4
  • 56
    • 41649115887 scopus 로고    scopus 로고
    • Discovery of novel targets with high throughput RNA interference screening
    • Kassner, P.D. Discovery of novel targets with high throughput RNA interference screening. Comb. Chem. High Throughput Screen, 2008, 11(3), 175-184.
    • (2008) Comb. Chem. High Throughput Screen , vol.11 , Issue.3 , pp. 175-184
    • Kassner, P.D.1
  • 59
    • 33748050780 scopus 로고    scopus 로고
    • Hypoxia-inducible factor-1 inhibition in combination with temozolomide treatment exhibits robust antitumor efficacy in vivo
    • Li, L.; Lin, X.; Shoemaker, A.R.; Albert, D.H.; Fesik, S.W.; Shen, Y. Hypoxia-inducible factor-1 inhibition in combination with temozolomide treatment exhibits robust antitumor efficacy in vivo. Clin. Cancer Res., 2006, 12(15), 4747-4754.
    • (2006) Clin. Cancer Res , vol.12 , Issue.15 , pp. 4747-4754
    • Li, L.1    Lin, X.2    Shoemaker, A.R.3    Albert, D.H.4    Fesik, S.W.5    Shen, Y.6
  • 60
    • 1242285120 scopus 로고    scopus 로고
    • SCL interacts with VEGF to suppress apoptosis at the onset of hematopoiesis
    • Martin, R.; Lahlil, R.; Damert, A.; Miquerol, L.; Nagy, A.; Keller, G.; Hoang, T. SCL interacts with VEGF to suppress apoptosis at the onset of hematopoiesis. Development, 2004, 131(3), 693-702.
    • (2004) Development , vol.131 , Issue.3 , pp. 693-702
    • Martin, R.1    Lahlil, R.2    Damert, A.3    Miquerol, L.4    Nagy, A.5    Keller, G.6    Hoang, T.7
  • 62
    • 2342436339 scopus 로고    scopus 로고
    • Hypomorphic expression of Dkk1 in the doubleridge mouse: Dose dependence and compensatory interactions with Lrp6
    • MacDonald, B.T.; Adamska, M.; Meisler, M.H. Hypomorphic expression of Dkk1 in the doubleridge mouse: dose dependence and compensatory interactions with Lrp6. Development, 2004, 1(11), 2543-2552.
    • (2004) Development , vol.1 , Issue.11 , pp. 2543-2552
    • Macdonald, B.T.1    Adamska, M.2    Meisler, M.H.3
  • 63
    • 33947278974 scopus 로고    scopus 로고
    • Genome maintenance defects in cultured cells and mice following partial inactivation of the essential cell cycle checkpoint gene Hus1
    • Levitt, P.S.; Zhu, M.; Cassano, A.; Yazinski, S.A.; Liu, H.; Darfler, J.; Peters, R.M.; Weiss, R.S. Genome maintenance defects in cultured cells and mice following partial inactivation of the essential cell cycle checkpoint gene Hus1. Mol. Cell Biol., 2007, 27(6), 2189-2201.
    • (2007) Mol. Cell Biol , vol.27 , Issue.6 , pp. 2189-2201
    • Levitt, P.S.1    Zhu, M.2    Cassano, A.3    Yazinski, S.A.4    Liu, H.5    Darfler, J.6    Peters, R.M.7    Weiss, R.S.8
  • 64
    • 33644767315 scopus 로고    scopus 로고
    • Normal cells, but not cancer cells, survive severe Plk1 depletion
    • Liu, X.; Lei, M.; Erikson, R.L. Normal cells, but not cancer cells, survive severe Plk1 depletion. Mol. Cell Biol., 2006, 26(6), 2093-2108.
    • (2006) Mol. Cell Biol , vol.26 , Issue.6 , pp. 2093-2108
    • Liu, X.1    Lei, M.2    Erikson, R.L.3
  • 68
    • 42449139634 scopus 로고    scopus 로고
    • Biology-inspired synthesis of compound libraries
    • Kaiser, M.; Wetzel, S.; Kumar, K.; Waldmann, H. Biology-inspired synthesis of compound libraries. Cell Mol. Life Sci., 2008, 65(7-8), 1186-1201.
    • (2008) Cell Mol. Life Sci , vol.65 , Issue.7-8 , pp. 1186-1201
    • Kaiser, M.1    Wetzel, S.2    Kumar, K.3    Waldmann, H.4
  • 69
    • 11144294717 scopus 로고    scopus 로고
    • Chemical genetics for therapeutic target mining
    • Shim, J.S.; Kwon, H. J. Chemical genetics for therapeutic target mining. Expert Opin. Ther. Targets, 2004, 8(6), 653-661.
    • (2004) Expert Opin. Ther. Targets , vol.8 , Issue.6 , pp. 653-661
    • Shim, J.S.1    Kwon, H.J.2
  • 70
    • 0031710509 scopus 로고    scopus 로고
    • Chemical genetics resulting from a passion for synthetic organic chemistry
    • Schreiber, S.L. Chemical genetics resulting from a passion for synthetic organic chemistry. Bioorg. Med. Chem., 1998, 6(8), 1127-1152.
    • (1998) Bioorg. Med. Chem , vol.6 , Issue.8 , pp. 1127-1152
    • Schreiber, S.L.1
  • 72
    • 54349088758 scopus 로고    scopus 로고
    • Chemical genetic analysis of FOXO nuclear-cytoplasmic shuttling by using image-based cell screening
    • Zanella, F.; Rosado, A.; García, B.; Carnero, A.; Link, W. Chemical genetic analysis of FOXO nuclear-cytoplasmic shuttling by using image-based cell screening. Chembiochem., 2008, 9(14), 2229-2237.
    • (2008) Chembiochem , vol.9 , Issue.14 , pp. 2229-2237
    • Zanella, F.1    Rosado, A.2    García, B.3    Carnero, A.4    Link, W.5
  • 75
    • 34250216344 scopus 로고    scopus 로고
    • Image-based multivariate profiling of drug responses from single cells
    • Loo, L.H.; Wu, L.F.; Altschuler, S.J. Image-based multivariate profiling of drug responses from single cells. Nat. Methods, 2007, 4(5), 445-453.
    • (2007) Nat. Methods , vol.4 , Issue.5 , pp. 445-453
    • Loo, L.H.1    Wu, L.F.2    Altschuler, S.J.3
  • 76
    • 0029748326 scopus 로고    scopus 로고
    • Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes
    • Schena, M.; Shalon, D.; Heller, R.; Chai, A.; Brown, P.O.; Davis, R.W. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA, 1996, 93(20), 10614-10619.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , Issue.20 , pp. 10614-10619
    • Schena, M.1    Shalon, D.2    Heller, R.3    Chai, A.4    Brown, P.O.5    Davis, R.W.6
  • 79
    • 70449389190 scopus 로고    scopus 로고
    • Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles
    • Li, Z.; Su, Z.; Wen, Z.; Shi, L.; Chen, T. Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles. BMC Bioinformatics, 2009, 10 (Suppl 11), S12.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 11
    • Li, Z.1    Su, Z.2    Wen, Z.3    Shi, L.4    Chen, T.5
  • 83
    • 71049131864 scopus 로고    scopus 로고
    • Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation
    • Ha, KCh.; Coulombe-Huntington, J.; Majewski, J. Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation. BMC Genomics, 2009, 10, 519.
    • (2009) BMC Genomics , vol.10 , pp. 519
    • Ha, K.C.1    Coulombe-Huntington, J.2    Majewski, J.3
  • 84
    • 77950490438 scopus 로고    scopus 로고
    • MADS+: Discovery of differential splicing events from Affymetrix exon junction array data
    • Shen, S.; Warzecha, C.C.; Carstens, R.P.; Xing, Y. MADS+: discovery of differential splicing events from Affymetrix exon junction array data. Bioinformatics, 2009, 26(2), 268-269.
    • (2009) Bioinformatics , vol.26 , Issue.2 , pp. 268-269
    • Shen, S.1    Warzecha, C.C.2    Carstens, R.P.3    Xing, Y.4
  • 85
    • 70349671437 scopus 로고    scopus 로고
    • Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis
    • Chen, Y.; Gelfond, J.A.; McManus, L.M.; Shireman, P.K. Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics, 2009, 10, 407.
    • (2009) BMC Genomics , vol.10 , pp. 407
    • Chen, Y.1    Gelfond, J.A.2    McManus, L.M.3    Shireman, P.K.4
  • 86
    • 65849488472 scopus 로고    scopus 로고
    • Intra-platform repeatability and inter-platform comparability of microRNA microarray technology
    • Sato, F.; Tsuchiya, S.; Terasawa, K.; Tsujimoto, G. Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One, 2009, 4(5), e5540.
    • (2009) PLoS One , vol.4 , Issue.5
    • Sato, F.1    Tsuchiya, S.2    Terasawa, K.3    Tsujimoto, G.4
  • 87
    • 45849087630 scopus 로고    scopus 로고
    • High throughput gene expression measurement with real time PCR in a microfluidic dynamic array
    • Spurgeon, S.L.; Jones, R.C.; Ramakrishnan, R. High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS One, 2008, 3(2), e1662.
    • (2008) PLoS One , vol.3 , Issue.2
    • Spurgeon, S.L.1    Jones, R.C.2    Ramakrishnan, R.3
  • 88
    • 68149170798 scopus 로고    scopus 로고
    • Resolving cell population heterogeneity: Real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples
    • Diercks, A.; Kostner, H.; Ozinsky, A. Resolving cell population heterogeneity: real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples. PLoS One, 2009, 4(7), e6326.
    • (2009) PLoS One , vol.4 , Issue.7
    • Diercks, A.1    Kostner, H.2    Ozinsky, A.3
  • 91
    • 30944450977 scopus 로고    scopus 로고
    • Organ messenger ribonucleic acid and plasma proteome changes in the adjuvant-induced arthritis model: Responses to disease induction and therapy with the estrogen receptor-beta selective agonist ERB-041
    • Follettie, M.T.; Pinard, M.; Keith, J.C Jr.; Wang, L.; Chelsky, D.; Hayward, C.; Kearney, P.; Thibault, P.; Paramithiotis, E.; Dorner, A.J.; Harris, H.A. Organ messenger ribonucleic acid and plasma proteome changes in the adjuvant-induced arthritis model: responses to disease induction and therapy with the estrogen receptor-beta selective agonist ERB-041. Endocrinology, 2006, 147(2), 714-723.
    • (2006) Endocrinology , vol.147 , Issue.2 , pp. 714-723
    • Follettie, M.T.1    Pinard, M.2    Keith Jr., J.C.3    Wang, L.4    Chelsky, D.5    Hayward, C.6    Kearney, P.7    Thibault, P.8    Paramithiotis, E.9    Dorner, A.J.10    Harris, H.A.11
  • 92
    • 11144355440 scopus 로고    scopus 로고
    • Applications of microarrays with toxicologically relevant genes (tox genes) for the evaluation of chemical toxicants in Sprague Dawley rats in vivo and human hepatocytes in vitro
    • Kier, L.D.; Neft, R.; Tang, L.; Suizu, R.; Cook, T.; Onsurez, K.; Tiegler, K.; Sakai, Y.; Ortiz, M.; Nolan, T.; Sankar, U.; Li, A.P. Applications of microarrays with toxicologically relevant genes (tox genes) for the evaluation of chemical toxicants in Sprague Dawley rats in vivo and human hepatocytes in vitro. Mutat. Res., 2004, 549(1-2), 101-113.
    • (2004) Mutat. Res , vol.549 , Issue.1-2 , pp. 101-113
    • Kier, L.D.1    Neft, R.2    Tang, L.3    Suizu, R.4    Cook, T.5    Onsurez, K.6    Tiegler, K.7    Sakai, Y.8    Ortiz, M.9    Nolan, T.10    Sankar, U.11    Li, A.P.12
  • 93
    • 61349162301 scopus 로고    scopus 로고
    • Pharmacogenomic approaches in clinical studies to identify biomarkers of safety and efficacy
    • Burczynski, M.E. Pharmacogenomic approaches in clinical studies to identify biomarkers of safety and efficacy. Toxicol. Lett., 2009, 186(1), 18-21.
    • (2009) Toxicol. Lett , vol.186 , Issue.1 , pp. 18-21
    • Burczynski, M.E.1
  • 97
    • 0242287052 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in DNA microarrays
    • Storey, J.D.; Tibshirani, R. Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods Mol. Biol., 2003, 224, 149-157.
    • (2003) Methods Mol. Biol , vol.224 , pp. 149-157
    • Storey, J.D.1    Tibshirani, R.2
  • 98
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen, M.B.; Spellman, P.T.; Brown, P.O.; Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 1998, 95(25), 14863-14868.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , Issue.25 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 101
    • 0036682376 scopus 로고    scopus 로고
    • Meta-analysis of microarrays: Interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer
    • Rhodes, D.R.; Barrette, T.R.; Rubin, M.A.; Ghosh, D.; Chinnaiyan, A. M. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer Cancer Res., 2002, 62(15), 4427-4433.
    • (2002) Cancer Res , vol.62 , Issue.15 , pp. 4427-4433
    • Rhodes, D.R.1    Barrette, T.R.2    Rubin, M.A.3    Ghosh, D.4    Chinnaiyan, A.M.5
  • 102
    • 3042694117 scopus 로고    scopus 로고
    • Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
    • Rhodes, D.R.; Yu, J.; Shanker, K.; Deshpande, N.; Varambally, R.; Ghosh, D.; Barrette, T.; Pandey, A.; Chinnaiyan, A.M. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc. Natl. Acad. Sci. USA, 2004, 101(25), 9309-9314.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , Issue.25 , pp. 9309-9314
    • Rhodes, D.R.1    Yu, J.2    Shanker, K.3    Deshpande, N.4    Varambally, R.5    Ghosh, D.6    Barrette, T.7    Pandey, A.8    Chinnaiyan, A.M.9
  • 103
    • 60949083872 scopus 로고    scopus 로고
    • Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer
    • Thomassen, M.; Tan, Q.; Kruse, T.A. Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer. BMC Cancer, 2008, 8, 394.
    • (2008) BMC Cancer , vol.8 , pp. 394
    • Thomassen, M.1    Tan, Q.2    Kruse, T.A.3
  • 107
    • 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
  • 108
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi, U.; Wang, Z.; Waern, K.; Shou, C.; Raha, D.; Gerstein, M.; Snyder, M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 2008, 320(5881), 1344-1349.
    • (2008) Science , vol.320 , Issue.5881 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 109
    • 0141920354 scopus 로고    scopus 로고
    • Comparing protein abundance and mRNA expression levels on a genomic scale
    • Greenbaum, D.; Colangelo, C.; Williams, K.; Gerstein, M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol., 2003, 4(9), 117.
    • (2003) Genome Biol , vol.4 , Issue.9 , pp. 117
    • Greenbaum, D.1    Colangelo, C.2    Williams, K.3    Gerstein, M.4
  • 110
    • 33645813378 scopus 로고    scopus 로고
    • Mass spectrometry and protein analysis
    • Domon, B.; Aebersold, R. Mass spectrometry and protein analysis. Science, 2006, 312(5771), 212-217.
    • (2006) Science , vol.312 , Issue.5771 , pp. 212-217
    • Domon, B.1    Aebersold, R.2
  • 111
    • 0024438708 scopus 로고
    • Electrospray ionization for mass spectrometry of large biomolecules
    • Fenn, J.B. Electrospray ionization for mass spectrometry of large biomolecules. Science, 1989, 246(4926), 64-71.
    • (1989) Science , vol.246 , Issue.4926 , pp. 64-71
    • Fenn, J.B.1
  • 112
    • 0024289037 scopus 로고
    • Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons
    • Karas, M.; Hillenkamp, F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem., 1988, 60(20), 2299-2301.
    • (1988) Anal. Chem , vol.60 , Issue.20 , pp. 2299-2301
    • Karas, M.1    Hillenkamp, F.2
  • 113
    • 0033051101 scopus 로고    scopus 로고
    • Direct analysis of protein complexes using mass spectrometry. Nat
    • Link, A.J. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol., 1999, 17(7), 676-682.
    • (1999) Biotechnol , vol.17 , Issue.7 , pp. 676-682
    • Link, A.J.1
  • 114
    • 3042789073 scopus 로고    scopus 로고
    • Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
    • Syka, J.E. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA, 2004, 101(26), 9528-9533.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , Issue.26 , pp. 9528-9533
    • Syka, J.E.1
  • 115
    • 0037398266 scopus 로고    scopus 로고
    • Interfacing the orbitrap mass analyzer to an electrospray ion source
    • Hardman, M.; Makarov A.A. Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal. Chem., 2003, 75(7), 1699-6705.
    • (2003) Anal. Chem , vol.75 , Issue.7 , pp. 1699-6705
    • Hardman, M.1    Makarov, A.A.2
  • 116
    • 0000857494 scopus 로고
    • An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
    • Eng, J.K.; McCormack, A.L.; Yates, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrometry, 1994, 5(11), 976-989.
    • (1994) J. Am. Soc. Mass Spectrometry , vol.5 , Issue.11 , pp. 976-989
    • Eng, J.K.1    McCormack, A.L.2    Yates, J.R.3
  • 117
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D.N. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis, 1999, 20(18), 3551-3567.
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1
  • 118
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong, S.E. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics, 2002, 1(5), 376-386.
    • (2002) Mol. Cell Proteomics , vol.1 , Issue.5 , pp. 376-386
    • Ong, S.E.1
  • 119
    • 0032875697 scopus 로고    scopus 로고
    • Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
    • Gygi, S.P. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol., 1999, 17(10), 994-999.
    • (1999) Nat. Biotechnol , vol.17 , Issue.10 , pp. 994-999
    • Gygi, S.P.1
  • 120
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P.L. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics, 2004, 3(12), 1154-1169.
    • (2004) Mol. Cell Proteomics , vol.3 , Issue.12 , pp. 1154-1169
    • Ross, P.L.1
  • 121
    • 0035384687 scopus 로고    scopus 로고
    • Proteolytic 18O labeling for comparative proteomics: Model studies with two serotypes of adenovirus
    • Yao, X. Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal. Chem., 2001, 73(13), 2836-2842.
    • (2001) Anal. Chem , vol.73 , Issue.13 , pp. 2836-2842
    • Yao, X.1
  • 122
    • 10744233766 scopus 로고    scopus 로고
    • Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards
    • Wang, W.; Zhou, H.; Lin, H.; Roy, S.; Shaler, T. A.; Hill, L. R.; Norton, S.; Kumar, P.; Anderle, M.; Becker, C. H. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem., 2003, 75, 4818-4826.
    • (2003) Anal. Chem , vol.75 , pp. 4818-4826
    • Wang, W.1    Zhou, H.2    Lin, H.3    Roy, S.4    Shaler, T.A.5    Hill, L.R.6    Norton, S.7    Kumar, P.8    Anderle, M.9    Becker, C.H.10
  • 124
    • 0034624002 scopus 로고    scopus 로고
    • Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways
    • Pandey, A.; Fernandez, M. M.; Steen, H.; Blagoev, B.; Nielsen, M. M.; Roche, S.; Mann, M.; Lodish, H. F. Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways. J. Biol. Chem., 2000, 275, 38633-38639.
    • (2000) J. Biol. Chem , vol.275 , pp. 38633-38639
    • Pandey, A.1    Fernandez, M.M.2    Steen, H.3    Blagoev, B.4    Nielsen, M.M.5    Roche, S.6    Mann, M.7    Lodish, H.F.8
  • 125
    • 30544443201 scopus 로고    scopus 로고
    • Identification of phosphorylation sites using microimmobilized metal affinity chromatography
    • Corthals, G. L.; Aebersold, R.; Goodlett, D. R. Identification of phosphorylation sites using microimmobilized metal affinity chromatography. Methods Enzymol., 2005, 405, 66-81.
    • (2005) Methods Enzymol , vol.405 , pp. 66-81
    • Corthals, G.L.1    Aebersold, R.2    Goodlett, D.R.3
  • 127
    • 3242688830 scopus 로고    scopus 로고
    • Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns
    • Pinkse, M. W.; Uitto, P. M.; Hilhorst, M. J.; Ooms, B.; Heck, A. J. Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. Anal. Chem., 2004, 76, 3935-3943.
    • (2004) Anal. Chem , vol.76 , pp. 3935-3943
    • Pinkse, M.W.1    Uitto, P.M.2    Hilhorst, M.J.3    Ooms, B.4    Heck, A.J.5
  • 129
    • 38049035341 scopus 로고    scopus 로고
    • Global profiling of phosphopeptides by titania affinity enrichment
    • Wu, J.; Shakey, Q.; Liu, W.; Schuller, A.; Follettie, M. T. Global profiling of phosphopeptides by titania affinity enrichment. J. Proteome Res., 2007, 6, 4684-4689.
    • (2007) J. Proteome Res , vol.6 , pp. 4684-4689
    • Wu, J.1    Shakey, Q.2    Liu, W.3    Schuller, A.4    Follettie, M.T.5
  • 130
    • 34250722602 scopus 로고    scopus 로고
    • Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks
    • Wolf-Yadlin, A.; Hautaniemi, S.; Lauffenburger, D. A.; White, F. M. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc. Natl. Acad. Sci. USA, 2007, 104, 5860-5865.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 5860-5865
    • Wolf-Yadlin, A.1    Hautaniemi, S.2    Lauffenburger, D.A.3    White, F.M.4
  • 132
    • 3042789073 scopus 로고    scopus 로고
    • Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry
    • Syka, J. E.; Coon, J. J.; Schroeder, M. J.; Shabanowitz, J.; Hunt, D. F. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA, 2004, 101, 9528-9533.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 9528-9533
    • Syka, J.E.1    Coon, J.J.2    Schroeder, M.J.3    Shabanowitz, J.4    Hunt, D.F.5
  • 134
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics, 2002, 1, 376-386.
    • (2002) Mol. Cell Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 137
    • 0000325341 scopus 로고
    • On Lines and Planes of Closest Fit to Systems of Points in Space
    • Pearson, K. On Lines and Planes of Closest Fit to Systems of Points in Space. Philos. Mag., 1901, 2 (6), 559-572.
    • (1901) Philos. Mag , vol.2 , Issue.6 , pp. 559-572
    • Pearson, K.1
  • 139
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: A database on transcription factors and their DNA binding sites
    • Wingender, E.; Dietze, P.; Karas, H.; Knüppel, R. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res., 1996, 24(1), 238-241.
    • (1996) Nucleic Acids Res , vol.24 , Issue.1 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knüppel, R.4


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