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Volumn 8, Issue 21, 2008, Pages 4453-4465

Towards functional phosphoproteomics by mapping differential phosphorylation events in signaling networks

Author keywords

Mass spectrometry; Phosphorylation; Quantitative phosphoproteomics; Signaling networks; Systems biology

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR KINASE INHIBITOR; GEFITINIB; PHOSPHOTRANSFERASE INHIBITOR; PROTEIN KINASE;

EID: 55849107369     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800175     Document Type: Review
Times cited : (48)

References (135)
  • 1
    • 0036198435 scopus 로고    scopus 로고
    • Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
    • Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J. et al., Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 2002, 20, 301-305.
    • (2002) Nat. Biotechnol , vol.20 , pp. 301-305
    • Ficarro, S.B.1    McCleland, M.L.2    Stukenberg, P.T.3    Burke, D.J.4
  • 2
    • 35348839586 scopus 로고    scopus 로고
    • PhosphoPep-a phosphoproteome resource for systems biology research in Drosophila Kc167 cells
    • Bodenmiller, B., Malmstrom, J., Gerrits, B., Campbell, D. et al., PhosphoPep-a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Mol. Syst. Biol. 2007, 3, 139.
    • (2007) Mol. Syst. Biol , vol.3 , pp. 139
    • Bodenmiller, B.1    Malmstrom, J.2    Gerrits, B.3    Campbell, D.4
  • 3
    • 33746730389 scopus 로고    scopus 로고
    • Phosphoproteomic approaches to elucidate cellular signaling networks
    • Schmelzle, K., White, F. M., Phosphoproteomic approaches to elucidate cellular signaling networks. Curr. Opin. Biotechnol. 2006, 17, 406-414.
    • (2006) Curr. Opin. Biotechnol , vol.17 , pp. 406-414
    • Schmelzle, K.1    White, F.M.2
  • 4
    • 0036605185 scopus 로고    scopus 로고
    • Analysis of protein phosphorylation using mass spectrometry: Deciphering the phosphoproteome
    • Mann, M., Ong, S. E., Grønborg, M., Steen, H. et al., Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends Biotechnol. 2002, 20, 261-268.
    • (2002) Trends Biotechnol , vol.20 , pp. 261-268
    • Mann, M.1    Ong, S.E.2    Grønborg, M.3    Steen, H.4
  • 5
    • 43849091451 scopus 로고    scopus 로고
    • Hydrophilic-interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection
    • McNulty, D. E., Annan, R. S., Hydrophilic-interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection. Mol. Cell. Proteomics 2008, 7, 971-980.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 971-980
    • McNulty, D.E.1    Annan, R.S.2
  • 6
    • 34249678458 scopus 로고    scopus 로고
    • Quantitative proteomic assessment of very early cellular signaling events
    • Dengjel, J., Akimov, V., Olsen, J. V., Bunkenborg, J. et al., Quantitative proteomic assessment of very early cellular signaling events. Nat. Biotechnol. 2007, 25, 566-568.
    • (2007) Nat. Biotechnol , vol.25 , pp. 566-568
    • Dengjel, J.1    Akimov, V.2    Olsen, J.V.3    Bunkenborg, J.4
  • 7
    • 34250878954 scopus 로고    scopus 로고
    • Mechanisms of specificity in protein phosphorylation
    • Ubersax, J. A., Ferrell, J. E., Jr., Mechanisms of specificity in protein phosphorylation. Nat. Rev. Mol. Cell. Biol. 2007, 8, 530-541.
    • (2007) Nat. Rev. Mol. Cell. Biol , vol.8 , pp. 530-541
    • Ubersax, J.A.1    Ferrell Jr., J.E.2
  • 8
    • 33646266474 scopus 로고    scopus 로고
    • Conformational changes in protein loops and helices induced by posttranslational phosphorylation
    • Groban, E. S., Narayanan, A., Jacobson, M. P., Conformational changes in protein loops and helices induced by posttranslational phosphorylation. PLoS Comput. Biol. 2006, 2, e32.
    • (2006) PLoS Comput. Biol , vol.2
    • Groban, E.S.1    Narayanan, A.2    Jacobson, M.P.3
  • 9
    • 33846671062 scopus 로고    scopus 로고
    • Tuning bulk electrostatics to regulate protein function
    • Serber, Z., Ferrell, J. E., Jr., Tuning bulk electrostatics to regulate protein function. Cell 2007, 128, 441-444.
    • (2007) Cell , vol.128 , pp. 441-444
    • Serber, Z.1    Ferrell Jr., J.E.2
  • 10
    • 33846686408 scopus 로고    scopus 로고
    • A mechanism for cell-cycle regulation of MAP kinase signaling in a yeast differentiation pathway
    • Strickfaden, S. C., Winters, M. J., Ben-Ari, G., Lamson, R. E. et al., A mechanism for cell-cycle regulation of MAP kinase signaling in a yeast differentiation pathway. Cell 2007, 128, 519-531.
    • (2007) Cell , vol.128 , pp. 519-531
    • Strickfaden, S.C.1    Winters, M.J.2    Ben-Ari, G.3    Lamson, R.E.4
  • 12
    • 33846908953 scopus 로고    scopus 로고
    • Ding, S. J., Qian, W. J., Smith, R. D., Quantitative proteomic approaches for studying phosphotyrosine signaling. Expert Rev. Proteomics 2007, 4, 13-23.
    • Ding, S. J., Qian, W. J., Smith, R. D., Quantitative proteomic approaches for studying phosphotyrosine signaling. Expert Rev. Proteomics 2007, 4, 13-23.
  • 13
    • 26844576371 scopus 로고    scopus 로고
    • Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules
    • Zhang, Y., Wolf-Yadlin, A., Ross, P. L., Pappin, D. J. et al., Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell. Proteomics 2005, 4, 1240-1250.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 1240-1250
    • Zhang, Y.1    Wolf-Yadlin, A.2    Ross, P.L.3    Pappin, D.J.4
  • 14
    • 34250316558 scopus 로고    scopus 로고
    • Quantitative proteomic analysis of phosphotyrosine-mediated cellular signaling networks
    • Zhang, Y., Wolf-Yadlin, A., White, F. M., Quantitative proteomic analysis of phosphotyrosine-mediated cellular signaling networks. Methods Mol. Biol. 2007, 359, 203-212.
    • (2007) Methods Mol. Biol , vol.359 , pp. 203-212
    • Zhang, Y.1    Wolf-Yadlin, A.2    White, F.M.3
  • 15
    • 42649123723 scopus 로고    scopus 로고
    • Defining the specificity space of the human src-homology 2 domain
    • Huang, H., Li, L., Wu, C., Schibli, D. et al., Defining the specificity space of the human src-homology 2 domain. Mol. Cell. Proteomics 2007, 7, 768-784.
    • (2007) Mol. Cell. Proteomics , vol.7 , pp. 768-784
    • Huang, H.1    Li, L.2    Wu, C.3    Schibli, D.4
  • 16
    • 30544449081 scopus 로고    scopus 로고
    • A quantitative protein interaction network for the ErbB receptors using protein microarrays
    • Jones, R. B., Gordus, A., Krall, J. A., MacBeath, G., A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature 2006, 439, 168-174.
    • (2006) Nature , vol.439 , pp. 168-174
    • Jones, R.B.1    Gordus, A.2    Krall, J.A.3    MacBeath, G.4
  • 17
    • 33745185987 scopus 로고    scopus 로고
    • The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling
    • Liu, B. A., Jablonowski, K., Raina, M., Arce, M. et al., The human and mouse complement of SH2 domain proteins-establishing the boundaries of phosphotyrosine signaling. Mol. Cell 2006, 22, 851-868.
    • (2006) Mol. Cell , vol.22 , pp. 851-868
    • Liu, B.A.1    Jablonowski, K.2    Raina, M.3    Arce, M.4
  • 18
    • 34250641161 scopus 로고    scopus 로고
    • High-throughput phosphotyrosine profiling using SH2 domains
    • Machida, K., Thompson, C. M., Dierck, K., Jablonowski, K. et al., High-throughput phosphotyrosine profiling using SH2 domains. Mol. Cell 2007, 26, 899-915.
    • (2007) Mol. Cell , vol.26 , pp. 899-915
    • Machida, K.1    Thompson, C.M.2    Dierck, K.3    Jablonowski, K.4
  • 19
    • 33847355217 scopus 로고    scopus 로고
    • Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate
    • Santos, S. D., Verveer, P. J., Bastiaens, P. I., Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Nat. Cell Biol. 2007, 9, 324-330.
    • (2007) Nat. Cell Biol , vol.9 , pp. 324-330
    • Santos, S.D.1    Verveer, P.J.2    Bastiaens, P.I.3
  • 20
    • 35448964335 scopus 로고    scopus 로고
    • Spatial regulation of Raf kinase signaling by RKTG
    • Feng, L., Xie, X., Ding, Q., Luo, X. et al., Spatial regulation of Raf kinase signaling by RKTG. Proc. Natl. Acad. Sci. USA 2007, 104, 14348-14353.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 14348-14353
    • Feng, L.1    Xie, X.2    Ding, Q.3    Luo, X.4
  • 21
    • 34548304052 scopus 로고    scopus 로고
    • Lv, L. L., Liu, B. C., High-throughput antibody microarrays for quantitative proteomic analysis. Expert Rev. Proteomics 2007, 4, 505-513.
    • Lv, L. L., Liu, B. C., High-throughput antibody microarrays for quantitative proteomic analysis. Expert Rev. Proteomics 2007, 4, 505-513.
  • 22
    • 23744444911 scopus 로고    scopus 로고
    • Beernink, H. T., Nock, S., Challenges facing the development and use of protein chips to analyze the phosphoproteome. Expert Rev. Proteomics 2005, 2, 487-497.
    • Beernink, H. T., Nock, S., Challenges facing the development and use of protein chips to analyze the phosphoproteome. Expert Rev. Proteomics 2005, 2, 487-497.
  • 23
    • 33748573639 scopus 로고    scopus 로고
    • Charging it up: Global analysis of protein phosphorylation
    • Ptacek, J., Snyder, M., Charging it up: global analysis of protein phosphorylation. Trends Genet. 2006, 22, 545-554.
    • (2006) Trends Genet , vol.22 , pp. 545-554
    • Ptacek, J.1    Snyder, M.2
  • 24
    • 34547509284 scopus 로고    scopus 로고
    • Phosphoproteomic identification of targets of the Arabidopsis sucrose nonfermenting-like kinase SnRK2.8 reveals a connection to metabolic processes
    • Shin, R., Alvarez, S., Burch, A. Y., Jez, J. M., Schachtman, D. P., Phosphoproteomic identification of targets of the Arabidopsis sucrose nonfermenting-like kinase SnRK2.8 reveals a connection to metabolic processes. Proc. Natl. Acad. Sci. USA 2007, 104, 6460-6465.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 6460-6465
    • Shin, R.1    Alvarez, S.2    Burch, A.Y.3    Jez, J.M.4    Schachtman, D.P.5
  • 25
    • 42649116833 scopus 로고    scopus 로고
    • Proteomic studies of brassinosteroid signal transduction using prefractionation and 2-D DIGE
    • Tang, W., Deng, Z., Oses-Prieto, J. A., Suzuki, N. et al., Proteomic studies of brassinosteroid signal transduction using prefractionation and 2-D DIGE. Mol. Cell. Proteomics 2008, 7, 728-738.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 728-738
    • Tang, W.1    Deng, Z.2    Oses-Prieto, J.A.3    Suzuki, N.4
  • 26
    • 24944519450 scopus 로고    scopus 로고
    • Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns
    • Larsen, M. R., Thingholm, T. E., Jensen, O. N., Roepstorff, P., Jorgensen, T. J., Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns. Mol. Cell. Proteomics 2005, 4, 873-886.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 873-886
    • Larsen, M.R.1    Thingholm, T.E.2    Jensen, O.N.3    Roepstorff, P.4    Jorgensen, T.J.5
  • 27
    • 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
  • 28
    • 23144441172 scopus 로고    scopus 로고
    • Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry
    • Tao, W. A., Wollscheid, B., O'Brien, R., Eng, J. K. et al., Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat. Methods 2005, 2, 591-598.
    • (2005) Nat. Methods , vol.2 , pp. 591-598
    • Tao, W.A.1    Wollscheid, B.2    O'Brien, R.3    Eng, J.K.4
  • 29
    • 0035072715 scopus 로고    scopus 로고
    • A systematic approach to the analysis of protein phosphorylation
    • Zhou, H., Watts, J. D., Aebersold, R., A systematic approach to the analysis of protein phosphorylation. Nat. Biotechnol. 2001, 19, 375-378.
    • (2001) Nat. Biotechnol , vol.19 , pp. 375-378
    • Zhou, H.1    Watts, J.D.2    Aebersold, R.3
  • 30
    • 33847616949 scopus 로고    scopus 로고
    • Reproducible isolation of distinct, overlapping segments of the phosphoproteome
    • Bodenmiller, B., Mueller, L. N., Mueller, M., Domon, B., Aebersold, R., Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat. Methods 2007, 4, 231-237.
    • (2007) Nat. Methods , vol.4 , pp. 231-237
    • Bodenmiller, B.1    Mueller, L.N.2    Mueller, M.3    Domon, B.4    Aebersold, R.5
  • 31
  • 32
    • 33750456519 scopus 로고    scopus 로고
    • Global, in vivo, and site-specific phosphorylation dynamics in signaling networks
    • Olsen, J. V., Blagoev, B., Gnad, F., Macek, B. et al., Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127, 635-648.
    • (2006) Cell , vol.127 , pp. 635-648
    • Olsen, J.V.1    Blagoev, B.2    Gnad, F.3    Macek, B.4
  • 33
    • 36849065315 scopus 로고    scopus 로고
    • Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer
    • Rikova, K., Guo, A., Zeng, Q., Possemato, A. et al., Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 2007, 131, 1190-1203.
    • (2007) Cell , vol.131 , pp. 1190-1203
    • Rikova, K.1    Guo, A.2    Zeng, Q.3    Possemato, A.4
  • 34
    • 34548459741 scopus 로고    scopus 로고
    • Using phosphoproteomics to reveal signaling dynamics in plants
    • De la Fuente van Bentem, S., Hirt, H., Using phosphoproteomics to reveal signaling dynamics in plants. Trends Plant Sci. 2007, 12, 404-411.
    • (2007) Trends Plant Sci , vol.12 , pp. 404-411
    • De la Fuente van Bentem, S.1    Hirt, H.2
  • 35
    • 39749166860 scopus 로고    scopus 로고
    • Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation
    • Macek, B., Gnad, F., Soufi, B., Kumar, C. et al., Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell. Proteomics 2008, 7, 299-307.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 299-307
    • Macek, B.1    Gnad, F.2    Soufi, B.3    Kumar, C.4
  • 36
    • 34247325212 scopus 로고    scopus 로고
    • The serine/ threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis
    • Macek, B., Mijakovic, I., Olsen, J. V., Gnad, F. et al., The serine/ threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 2007, 6, 697-707.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 697-707
    • Macek, B.1    Mijakovic, I.2    Olsen, J.V.3    Gnad, F.4
  • 37
    • 33749828996 scopus 로고    scopus 로고
    • Automated phosphorylation site mapping
    • Jensen, O. N., Automated phosphorylation site mapping. Nat. Biotechnol. 2006, 24, 1226-1227.
    • (2006) Nat. Biotechnol , vol.24 , pp. 1226-1227
    • Jensen, O.N.1
  • 38
    • 34548392335 scopus 로고    scopus 로고
    • Analysis of protein phosphorylation on a proteome-scale
    • Collins, M. O., Yu, L., Choudhary, J. S., Analysis of protein phosphorylation on a proteome-scale. Proteomics 2007, 7, 2751-2768.
    • (2007) Proteomics , vol.7 , pp. 2751-2768
    • Collins, M.O.1    Yu, L.2    Choudhary, J.S.3
  • 39
    • 19444363756 scopus 로고    scopus 로고
    • Mass spectrometry-based quantitative proteomic profiling
    • Yan, W., Chen, S. S., Mass spectrometry-based quantitative proteomic profiling. Brief. Funct. Genomic. Proteomic. 2005, 4, 27-38.
    • (2005) Brief. Funct. Genomic. Proteomic , vol.4 , pp. 27-38
    • Yan, W.1    Chen, S.S.2
  • 40
    • 38649095599 scopus 로고    scopus 로고
    • An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
    • Mueller, L. N., Brusniak, M. Y., Mani, D. R., Aebersold, R., An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 2008, 7, 51-61.
    • (2008) J. Proteome Res , vol.7 , pp. 51-61
    • Mueller, L.N.1    Brusniak, M.Y.2    Mani, D.R.3    Aebersold, R.4
  • 41
    • 33749332751 scopus 로고    scopus 로고
    • Temporal dynamics of tyrosine phosphorylation in insulin signaling
    • Schmelzle, K., Kane, S., Gridley, S., Lienhard, G. E., White, F. M., Temporal dynamics of tyrosine phosphorylation in insulin signaling. Diabetes 2006, 55, 2171-2179.
    • (2006) Diabetes , vol.55 , pp. 2171-2179
    • Schmelzle, K.1    Kane, S.2    Gridley, S.3    Lienhard, G.E.4    White, F.M.5
  • 42
    • 0037795741 scopus 로고    scopus 로고
    • Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
    • Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., Gygi, S. P., Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 2003, 100, 6940-6945.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 6940-6945
    • Gerber, S.A.1    Rush, J.2    Stemman, O.3    Kirschner, M.W.4    Gygi, S.P.5
  • 43
    • 33745621292 scopus 로고    scopus 로고
    • Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: Determination of inhibitory phosphorylation status of cyclin-dependent kinases
    • Mayya, V., Rezual, K., Wu, L., Fong, M. B., Han, D. K., Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases. Mol. Cell. Proteomics 2006, 5, 1146-1157.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 1146-1157
    • Mayya, V.1    Rezual, K.2    Wu, L.3    Fong, M.B.4    Han, D.K.5
  • 44
    • 39749146978 scopus 로고    scopus 로고
    • Quantitative proteomic analysis of protein complexes: Concurrent identification of interactors and their state of phosphorylation
    • Pflieger, D., Junger, M. A., Muller, M., Rinner, O. et al., Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Mol. Cell. Proteomics 2008, 7, 326-346.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 326-346
    • Pflieger, D.1    Junger, M.A.2    Muller, M.3    Rinner, O.4
  • 45
    • 33847661220 scopus 로고    scopus 로고
    • Qualitative and quantitative analyses of protein phosphorylation in naive and stimulated mouse synaptosomal preparations
    • Munton, R. P., Tweedie-Cullen, R., Livingstone-Zatchej, M., Weinandy, F. et al., Qualitative and quantitative analyses of protein phosphorylation in naive and stimulated mouse synaptosomal preparations. Mol. Cell. Proteomics 2007, 6, 283-293.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 283-293
    • Munton, R.P.1    Tweedie-Cullen, R.2    Livingstone-Zatchej, M.3    Weinandy, F.4
  • 46
    • 35648996970 scopus 로고    scopus 로고
    • Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis
    • Niittylä, T., Fuglsang, A. T., Palmgren, M. G., Frommer, W. B., Schulze, W. X., Temporal analysis of sucrose-induced phosphorylation changes in plasma membrane proteins of Arabidopsis. Mol. Cell. Proteomics 2007, 6, 1711-1726.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1711-1726
    • Niittylä, T.1    Fuglsang, A.T.2    Palmgren, M.G.3    Frommer, W.B.4    Schulze, W.X.5
  • 47
    • 33845329203 scopus 로고    scopus 로고
    • Functional and quantitative proteomics using SILAC
    • Mann, M., Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 2006, 7, 952-958.
    • (2006) Nat. Rev. Mol. Cell Biol , vol.7 , pp. 952-958
    • Mann, M.1
  • 48
    • 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. et al., 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
  • 49
    • 34548356772 scopus 로고    scopus 로고
    • An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics
    • Van Hoof, D., Pinkse, M. W., Oostwaard, D. W., Mummery, C. L. et al., An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics. Nat. Methods 2007, 4, 677-678.
    • (2007) Nat. Methods , vol.4 , pp. 677-678
    • Van Hoof, D.1    Pinkse, M.W.2    Oostwaard, D.W.3    Mummery, C.L.4
  • 50
    • 42649132889 scopus 로고    scopus 로고
    • SILAC-labeling and proteome quantitation of mouse embryonic stem cells to a depth of 5111 proteins
    • Graumann, J., Hubner, N. C., Kim, J. B., Ko, K. et al., SILAC-labeling and proteome quantitation of mouse embryonic stem cells to a depth of 5111 proteins. Mol. Cell. Proteomics 2007, 7, 672-683.
    • (2007) Mol. Cell. Proteomics , vol.7 , pp. 672-683
    • Graumann, J.1    Hubner, N.C.2    Kim, J.B.3    Ko, K.4
  • 51
    • 45749144385 scopus 로고    scopus 로고
    • Stable isotopic labeling of amino acids in cultured primary neurons: Application to BDNF-dependent phosphotyrosine-associated signaling
    • Spellman, D. S., Deinhardt, K., Darie, C. C., Chao, M. V., Neubert, T. A., Stable isotopic labeling of amino acids in cultured primary neurons: Application to BDNF-dependent phosphotyrosine-associated signaling. Mol. Cell. Proteomics 2008, 7, 1067-1076.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 1067-1076
    • Spellman, D.S.1    Deinhardt, K.2    Darie, C.C.3    Chao, M.V.4    Neubert, T.A.5
  • 52
    • 44449124267 scopus 로고    scopus 로고
    • Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis
    • Cantin, G. T., Yi, W., Lu, B., Park, S. K. et al., Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. J. Proteome Res. 2008, 7, 1346-1351.
    • (2008) J. Proteome Res , vol.7 , pp. 1346-1351
    • Cantin, G.T.1    Yi, W.2    Lu, B.3    Park, S.K.4
  • 53
  • 54
    • 34547881522 scopus 로고    scopus 로고
    • Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma
    • Huang, P. H., Mukasa, A., Bonavia, R., Flynn, R. A. et al., Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc. Natl. Acad. Sci. USA 2007, 104, 12867-12872.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 12867-12872
    • Huang, P.H.1    Mukasa, A.2    Bonavia, R.3    Flynn, R.A.4
  • 55
    • 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
  • 56
    • 35648942133 scopus 로고    scopus 로고
    • 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease
    • Choe, L., D'Ascenzo, M., Relkin, N. R., Pappin, D. et al., 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics 2007, 7, 3651-3660.
    • (2007) Proteomics , vol.7 , pp. 3651-3660
    • Choe, L.1    D'Ascenzo, M.2    Relkin, N.R.3    Pappin, D.4
  • 57
    • 19944432197 scopus 로고    scopus 로고
    • Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
    • Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
    • (2004) Mol. Cell. Proteomics , vol.3 , pp. 1154-1169
    • Ross, P.L.1    Huang, Y.N.2    Marchese, J.N.3    Williamson, B.4
  • 58
    • 34547110110 scopus 로고    scopus 로고
    • Quantitative phospho-proteomics of early elicitor signaling in Arabidopsis
    • Benschop, J. J., Mohammed, S., O'Flaherty, M., Heck, A. J. et al., Quantitative phospho-proteomics of early elicitor signaling in Arabidopsis. Mol. Cell. Proteomics 2007, 6, 1198-1214.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 1198-1214
    • Benschop, J.J.1    Mohammed, S.2    O'Flaherty, M.3    Heck, A.J.4
  • 59
    • 0942265386 scopus 로고    scopus 로고
    • 15N-isotope labeling of plants: Using the greenhouse for structural proteomics
    • 15N-isotope labeling of plants: using the greenhouse for structural proteomics. Proteomics 2004, 4, 226-234.
    • (2004) Proteomics , vol.4 , pp. 226-234
    • Ippel, J.H.1    Pouvreau, L.2    Kroef, T.3    Gruppen, H.4
  • 62
    • 34249650777 scopus 로고    scopus 로고
    • Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thaliana
    • Huttlin, E. L., Hegeman, A. D., Harms, A. C., Sussman, M. R., Comparison of full versus partial metabolic labeling for quantitative proteomics analysis in Arabidopsis thaliana. Mol. Cell. Proteomics 2007, 6, 860-881.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 860-881
    • Huttlin, E.L.1    Hegeman, A.D.2    Harms, A.C.3    Sussman, M.R.4
  • 63
    • 30744432140 scopus 로고    scopus 로고
    • Cantin, G. T., Venable, J. D., Cociorva, D., Yates, J. R., 3rd, Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. J. Proteome Res. 2006, 5, 127-134.
    • Cantin, G. T., Venable, J. D., Cociorva, D., Yates, J. R., 3rd, Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. J. Proteome Res. 2006, 5, 127-134.
  • 64
    • 15944377809 scopus 로고    scopus 로고
    • Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway
    • Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P. et al., Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell. Proteomics 2005, 4, 310-327.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 310-327
    • Gruhler, A.1    Olsen, J.V.2    Mohammed, S.3    Mortensen, P.4
  • 65
    • 42649142332 scopus 로고    scopus 로고
    • Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses; application to cell signaling events of interferon- stimulated macrophages
    • Marcantonio, M., Trost, M., Courcelles, M., Desjardins, M., Thibault, P., Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses; application to cell signaling events of interferon- stimulated macrophages. Mol. Cell. Proteomics 2008, 7, 645-660.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 645-660
    • Marcantonio, M.1    Trost, M.2    Courcelles, M.3    Desjardins, M.4    Thibault, P.5
  • 66
    • 34548128405 scopus 로고    scopus 로고
    • Quantitative phosphoproteomic analysis of plasma membrane proteins reveals regulatory mechanisms of plant innate immune responses
    • Nühse, T. S., Bottrill, A. R., Jones, A. M., Peck, S. C., Quantitative phosphoproteomic analysis of plasma membrane proteins reveals regulatory mechanisms of plant innate immune responses. Plant J. 2007, 51, 931-940.
    • (2007) Plant J , vol.51 , pp. 931-940
    • Nühse, T.S.1    Bottrill, A.R.2    Jones, A.M.3    Peck, S.C.4
  • 67
    • 34250743173 scopus 로고    scopus 로고
    • Systematic discovery of in vivo phosphorylation networks
    • Linding, R., Jensen, L. J., Ostheimer, G. J., van Vugt, M. A. et al., Systematic discovery of in vivo phosphorylation networks. Cell 2007, 129, 1415-1426.
    • (2007) Cell , vol.129 , pp. 1415-1426
    • Linding, R.1    Jensen, L.J.2    Ostheimer, G.J.3    van Vugt, M.A.4
  • 68
    • 33750123615 scopus 로고    scopus 로고
    • Phosphoproteomics strategies for the functional analysis of signal transduction
    • Morandell, S., Stasyk, T., Grosstessner-Hain, K., Roitinger, E. et al., Phosphoproteomics strategies for the functional analysis of signal transduction. Proteomics 2006, 6, 4047-4056.
    • (2006) Proteomics , vol.6 , pp. 4047-4056
    • Morandell, S.1    Stasyk, T.2    Grosstessner-Hain, K.3    Roitinger, E.4
  • 69
    • 34249947699 scopus 로고    scopus 로고
    • ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
    • Matsuoka, S., Ballif, B. A., Smogorzewska, A., McDonald, E. R., 3rd et al., ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007, 316, 1160-1166.
    • (2007) Science , vol.316 , pp. 1160-1166
    • Matsuoka, S.1    Ballif, B.A.2    Smogorzewska, A.3    McDonald 3rd, E.R.4
  • 72
    • 38449110993 scopus 로고    scopus 로고
    • Quantitative time-resolved phosphoproteomic analysis of mast cell signaling
    • Cao, L., Yu, K., Banh, C., Nguyen, V. et al., Quantitative time-resolved phosphoproteomic analysis of mast cell signaling. J. Immunol. 2007, 179, 5864-5876.
    • (2007) J. Immunol , vol.179 , pp. 5864-5876
    • Cao, L.1    Yu, K.2    Banh, C.3    Nguyen, V.4
  • 73
    • 33746889808 scopus 로고    scopus 로고
    • Oda, K., Matsuoka, Y., Funahashi, A., Kitano, H., A comprehensive pathway map of epidermal growth factor receptor signaling. Mol. Syst. Biol. 2005, 1, 2005 0010.
    • Oda, K., Matsuoka, Y., Funahashi, A., Kitano, H., A comprehensive pathway map of epidermal growth factor receptor signaling. Mol. Syst. Biol. 2005, 1, 2005 0010.
  • 74
    • 36248968708 scopus 로고    scopus 로고
    • SnapShot: EGFR signaling pathway
    • Yarden, Y., Shilo, B. Z., SnapShot: EGFR signaling pathway. Cell 2007, 131, 1018.
    • (2007) Cell , vol.131 , pp. 1018
    • Yarden, Y.1    Shilo, B.Z.2
  • 75
    • 34249706373 scopus 로고    scopus 로고
    • Identification of endosomal epidermal growth factor receptor signaling targets by functional organelle proteomics
    • Stasyk, T., Schiefermeier, N., Skvortsov, S., Zwierzina, H. et al., Identification of endosomal epidermal growth factor receptor signaling targets by functional organelle proteomics. Mol. Cell. Proteomics 2007, 6, 908-922.
    • (2007) Mol. Cell. Proteomics , vol.6 , pp. 908-922
    • Stasyk, T.1    Schiefermeier, N.2    Skvortsov, S.3    Zwierzina, H.4
  • 76
    • 37049019067 scopus 로고    scopus 로고
    • Late endosomal traffic of the epidermal growth factor receptor ensures spatial and temporal fidelity of mitogen-activated protein kinase signaling
    • Taub, N., Teis, D., Ebner, H. L., Hess, M. W., Huber, L. A., Late endosomal traffic of the epidermal growth factor receptor ensures spatial and temporal fidelity of mitogen-activated protein kinase signaling. Mol. Biol. Cell. 2007, 18, 4698-4710.
    • (2007) Mol. Biol. Cell , vol.18 , pp. 4698-4710
    • Taub, N.1    Teis, D.2    Ebner, H.L.3    Hess, M.W.4    Huber, L.A.5
  • 77
    • 34548522775 scopus 로고    scopus 로고
    • Advances in proteomic workflows for systems biology
    • Malmstrom, J., Lee, H., Aebersold, R., Advances in proteomic workflows for systems biology. Curr. Opin. Biotechnol. 2007, 18, 378-384.
    • (2007) Curr. Opin. Biotechnol , vol.18 , pp. 378-384
    • Malmstrom, J.1    Lee, H.2    Aebersold, R.3
  • 78
    • 33745585792 scopus 로고    scopus 로고
    • Phosphoproteomic analysis of Her2/neu signaling and inhibition
    • Bose, R., Molina, H., Patterson, A. S., Bitok, J. K. et al., Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proc. Natl. Acad. Sci. USA 2006, 103, 9773-9778.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 9773-9778
    • Bose, R.1    Molina, H.2    Patterson, A.S.3    Bitok, J.K.4
  • 79
    • 33750696663 scopus 로고    scopus 로고
    • Effects of HER2 overexpression on cell signaling networks governing proliferation and migration
    • Wolf-Yadlin, A., Kumar, N., Zhang, Y., Hautaniemi, S. et al., Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol. Syst. Biol. 2006, 2, 54.
    • (2006) Mol. Syst. Biol , vol.2 , pp. 54
    • Wolf-Yadlin, A.1    Kumar, N.2    Zhang, Y.3    Hautaniemi, S.4
  • 80
    • 33846554088 scopus 로고    scopus 로고
    • Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data
    • Kumar, N., Wolf-Yadlin, A., White, F. M., Lauffenburger, D. A., Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput. Biol. 2007, 3, e4.
    • (2007) PLoS Comput. Biol , vol.3
    • Kumar, N.1    Wolf-Yadlin, A.2    White, F.M.3    Lauffenburger, D.A.4
  • 81
    • 36849068465 scopus 로고    scopus 로고
    • Evolvable signaling networks of receptor tyrosine kinases: Relevance of robustness to malignancy and to cancer therapy
    • Amit, I., Wides, R., Yarden, Y., Evolvable signaling networks of receptor tyrosine kinases: relevance of robustness to malignancy and to cancer therapy. Mol. Syst. Biol. 2007, 3, 151.
    • (2007) Mol. Syst. Biol , vol.3 , pp. 151
    • Amit, I.1    Wides, R.2    Yarden, Y.3
  • 82
    • 34249075147 scopus 로고    scopus 로고
    • MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling
    • Engelman, J. A., Zejnullahu, K., Mitsudomi, T., Song, Y. et al., MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science 2007, 316, 1039-1043.
    • (2007) Science , vol.316 , pp. 1039-1043
    • Engelman, J.A.1    Zejnullahu, K.2    Mitsudomi, T.3    Song, Y.4
  • 83
    • 37249066605 scopus 로고    scopus 로고
    • Uncovering therapeutic targets for glioblastoma: A systems biology approach
    • Huang, P. H., Cavenee, W. K., Furnari, F. B., White, F. M., Uncovering therapeutic targets for glioblastoma: a systems biology approach. Cell Cycle 2007, 6, 2750-2754.
    • (2007) Cell Cycle , vol.6 , pp. 2750-2754
    • Huang, P.H.1    Cavenee, W.K.2    Furnari, F.B.3    White, F.M.4
  • 84
    • 34948875686 scopus 로고    scopus 로고
    • Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors
    • Bantscheff, M., Eberhard, D., Abraham, Y., Bastuck, S. et al., Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 2007, 25, 1035-1044.
    • (2007) Nat. Biotechnol , vol.25 , pp. 1035-1044
    • Bantscheff, M.1    Eberhard, D.2    Abraham, Y.3    Bastuck, S.4
  • 85
    • 38049018155 scopus 로고    scopus 로고
    • A quantitative analysis of kinase inhibitor selectivity
    • Karaman, M. W., Herrgard, S., Treiber, D. K., Gallant, P. et al., A quantitative analysis of kinase inhibitor selectivity. Nat. Biotechnol. 2008, 26, 127-132.
    • (2008) Nat. Biotechnol , vol.26 , pp. 127-132
    • Karaman, M.W.1    Herrgard, S.2    Treiber, D.K.3    Gallant, P.4
  • 86
    • 85142163384 scopus 로고    scopus 로고
    • Zhou, Y., Cras-Méneur, C., Ohsugi, M., Stormo, G. D., Permutt, M. A., A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. Bioinformatics 2007, 23, 2073-2079.
    • Zhou, Y., Cras-Méneur, C., Ohsugi, M., Stormo, G. D., Permutt, M. A., A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. Bioinformatics 2007, 23, 2073-2079.
  • 87
    • 0034948896 scopus 로고    scopus 로고
    • A Bayesian framework for the analysis inferences of gene changes
    • Baldi, P., Long, A., A Bayesian framework for the analysis inferences of gene changes. Bioinformatics 2001, 17, 509-519.
    • (2001) Bioinformatics , vol.17 , pp. 509-519
    • Baldi, P.1    Long, A.2
  • 88
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V. G., Tibshirani, R., Chu, G., Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 2001, 98, 5116-5121.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 91
    • 16344371755 scopus 로고    scopus 로고
    • Indentifying differentially expressed genes from microarray experiments via statistic synthesis
    • Yang, Y. H., Xiao, Y., Segal, M., Indentifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics 2005, 21, 1084-1093.
    • (2005) Bioinformatics , vol.21 , pp. 1084-1093
    • Yang, Y.H.1    Xiao, Y.2    Segal, M.3
  • 92
    • 42649093228 scopus 로고    scopus 로고
    • Quantitative analysis of synaptic phosphorylation and protein expression
    • Trinidad, J. C., Thalhammer, A., Specht, C. G., Lynn, A. J. et al., Quantitative analysis of synaptic phosphorylation and protein expression. Mol. Cell. Proteomics 2008, 7, 684-696.
    • (2008) Mol. Cell. Proteomics , vol.7 , pp. 684-696
    • Trinidad, J.C.1    Thalhammer, A.2    Specht, C.G.3    Lynn, A.J.4
  • 93
    • 0036376993 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
    • Dudoit, S., Yang, Y. H., Callow, M. J., Speed, T. P., Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statist. Sinica 2002, 12, 111-139.
    • (2002) Statist. Sinica , vol.12 , pp. 111-139
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 95
    • 0002294347 scopus 로고
    • A simple sequentially rejective multiple test procedure
    • Holm, S., A simple sequentially rejective multiple test procedure. Scand. J. Stat. 1979, 6, 65-70.
    • (1979) Scand. J. Stat , vol.6 , pp. 65-70
    • Holm, S.1
  • 96
    • 0001677717 scopus 로고
    • Controlling the False Discovery Rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., Hochberg, Y., Controlling the False Discovery Rate: A practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 1995, 57, 289-300.
    • (1995) J. Roy. Statist. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 97
    • 0037187833 scopus 로고    scopus 로고
    • A mixture model approach for the analysis of microarray gene expression data
    • Allison, D. B., Gadbury, G. L., Heo, M., Fernández, J. R. et al., A mixture model approach for the analysis of microarray gene expression data. Comput. Statist. Data Anal. 2002, 39, 1-20.
    • (2002) Comput. Statist. Data Anal , vol.39 , pp. 1-20
    • Allison, D.B.1    Gadbury, G.L.2    Heo, M.3    Fernández, J.R.4
  • 98
    • 0034370950 scopus 로고    scopus 로고
    • On the adaptive control of the false discovery rate in multiple testing with independent statistics
    • Benjamini, Y., Hochberg, Y., On the adaptive control of the false discovery rate in multiple testing with independent statistics. J. Educa. Behav. Stat. 2000, 25, 60-83.
    • (2000) J. Educa. Behav. Stat , vol.25 , pp. 60-83
    • Benjamini, Y.1    Hochberg, Y.2
  • 99
    • 1642381468 scopus 로고    scopus 로고
    • Controlling the proportion of false positives (PFP) in multiple dependent tests
    • Fernando, R. L., Nettleton, D., Southey, B. R., Dekkers, J. C. M. et al., Controlling the proportion of false positives (PFP) in multiple dependent tests. Genetics 2004, 166, 611-619.
    • (2004) Genetics , vol.166 , pp. 611-619
    • Fernando, R.L.1    Nettleton, D.2    Southey, B.R.3    Dekkers, J.C.M.4
  • 101
    • 3042562270 scopus 로고    scopus 로고
    • Genomics, prior probability, and statistical tests of multiple hypotheses
    • Manly, K. F., Nettleton, D., Hwang, J. T., Genomics, prior probability, and statistical tests of multiple hypotheses. Genome Res. 2004, 14, 997-1001.
    • (2004) Genome Res , vol.14 , pp. 997-1001
    • Manly, K.F.1    Nettleton, D.2    Hwang, J.T.3
  • 102
    • 0035047910 scopus 로고    scopus 로고
    • A whole genome scan for quantitative trait loci affecting milk protein percentage in Israeli-Holstein cattle, by means of selective milk DNA pooling in a daughter design, using an adjusted false discovery rate criterion
    • Mosig, M. O., Lipkin, E., Khutoreskaya, G., Tchourzyna, E. et al., A whole genome scan for quantitative trait loci affecting milk protein percentage in Israeli-Holstein cattle, by means of selective milk DNA pooling in a daughter design, using an adjusted false discovery rate criterion. Genetics 2001, 157, 1683-1698.
    • (2001) Genetics , vol.157 , pp. 1683-1698
    • Mosig, M.O.1    Lipkin, E.2    Khutoreskaya, G.3    Tchourzyna, E.4
  • 103
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey, J. D., Tibshirani, R., Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 2003, 100, 9440-9445.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 104
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Storey, J. D., A direct approach to false discovery rates. J. R. Stat.Soc. 2002, 3, 479-498.
    • (2002) J. R. Stat.Soc , vol.3 , pp. 479-498
    • Storey, J.D.1
  • 105
    • 34147123145 scopus 로고    scopus 로고
    • The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments
    • Storey, J. D., Dai, J. Y., Leek, J. T., The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments. Biostatistics 2007, 8, 414-432.
    • (2007) Biostatistics , vol.8 , pp. 414-432
    • Storey, J.D.1    Dai, J.Y.2    Leek, J.T.3
  • 106
    • 32544433476 scopus 로고    scopus 로고
    • Extraction and analysis of differential gene expression
    • EDGE
    • Leek, J. T., Monsen, E., Dabney, A. R., Storey, J. D., EDGE: Extraction and analysis of differential gene expression. Bioinformatics 2006, 22, 507-508.
    • (2006) Bioinformatics , vol.22 , pp. 507-508
    • Leek, J.T.1    Monsen, E.2    Dabney, A.R.3    Storey, J.D.4
  • 107
    • 0034927555 scopus 로고    scopus 로고
    • Analysis of variance for gene expressionmicroarray data
    • Kerr, M. K., Martin, M., Churchill, G. A., Analysis of variance for gene expressionmicroarray data. J. Comput. Biol. 2000, 7, 819-837.
    • (2000) J. Comput. Biol , vol.7 , pp. 819-837
    • Kerr, M.K.1    Martin, M.2    Churchill, G.A.3
  • 108
    • 0035687554 scopus 로고    scopus 로고
    • Assessing gene significance from cDNA microarray expression data via mixed models
    • Wolfinger, R. D., Gibson, G., Wolfinger, E. D., Bennett, L. et al., Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol. 2001, 8, 625-637.
    • (2001) J Comput Biol , vol.8 , pp. 625-637
    • Wolfinger, R.D.1    Gibson, G.2    Wolfinger, E.D.3    Bennett, L.4
  • 109
    • 33749260517 scopus 로고    scopus 로고
    • A discussion of statistical methods for design and analysis of microarray experiments for plant scientists
    • Nettleton, D., A discussion of statistical methods for design and analysis of microarray experiments for plant scientists. Plant Cell 2006, 18, 2112-2121.
    • (2006) Plant Cell , vol.18 , pp. 2112-2121
    • Nettleton, D.1
  • 110
    • 0037433769 scopus 로고    scopus 로고
    • Statistical tests for identifying differentially expressed genes in time-course microarray experiments
    • Park, T., Yi, S. G., Lee, S., Lee, S. Y. et al., Statistical tests for identifying differentially expressed genes in time-course microarray experiments. Bioinformatics 2003, 19, 694-703.
    • (2003) Bioinformatics , vol.19 , pp. 694-703
    • Park, T.1    Yi, S.G.2    Lee, S.3    Lee, S.Y.4
  • 111
    • 34248145293 scopus 로고    scopus 로고
    • Significance analysis of microarray transcript levels in time series experiments
    • Di Camillo, B., Toffolo, G., Nair, S. K., Greenlund, L. J., Cobelli, C., Significance analysis of microarray transcript levels in time series experiments. BMC bioinformatics 2007, 8 Suppl 1, S10.
    • (2007) BMC bioinformatics , vol.8 , Issue.SUPPL. 1
    • Di Camillo, B.1    Toffolo, G.2    Nair, S.K.3    Greenlund, L.J.4    Cobelli, C.5
  • 112
    • 33947177672 scopus 로고    scopus 로고
    • Empirical comparison of tests for differential expression on time-series microarray experiments
    • Fischer, E. A., Friedman, M. A., Markey, M. K., Empirical comparison of tests for differential expression on time-series microarray experiments. Genomics 2007, 89, 460-470.
    • (2007) Genomics , vol.89 , pp. 460-470
    • Fischer, E.A.1    Friedman, M.A.2    Markey, M.K.3
  • 114
    • 0037101842 scopus 로고    scopus 로고
    • A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model
    • Xu, X. L., Olson, J. M., Zhao, L. P., A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model. Hum. Mol. Genet. 2002, 11, 1977-1985.
    • (2002) Hum. Mol. Genet , vol.11 , pp. 1977-1985
    • Xu, X.L.1    Olson, J.M.2    Zhao, L.P.3
  • 115
    • 33750414249 scopus 로고    scopus 로고
    • A multivariate empirical Bayes statistic for replicated microarray time course data
    • Tai, Y. C., Speed, T. P., A multivariate empirical Bayes statistic for replicated microarray time course data. Annals of Statistics 2006, 34, 2387-2412.
    • (2006) Annals of Statistics , vol.34 , pp. 2387-2412
    • Tai, Y.C.1    Speed, T.P.2
  • 116
    • 0141850391 scopus 로고    scopus 로고
    • Statistical significance analysis of longitudinal gene expression data
    • Guo, X., Qi, H., Verfaillie, C. M., Pan, W., Statistical significance analysis of longitudinal gene expression data. Bioinformatics 2003, 19, 1628-1635.
    • (2003) Bioinformatics , vol.19 , pp. 1628-1635
    • Guo, X.1    Qi, H.2    Verfaillie, C.M.3    Pan, W.4
  • 117
    • 33846036999 scopus 로고    scopus 로고
    • Hidden Markov models for microarray time course data in multiple biological conditions (with discussion)
    • Yuan, M., Kendziorski, C., Hidden Markov models for microarray time course data in multiple biological conditions (with discussion). J. Amer. Statist. Assoc. 2006, 101, 1323-1340.
    • (2006) J. Amer. Statist. Assoc , vol.101 , pp. 1323-1340
    • Yuan, M.1    Kendziorski, C.2
  • 118
    • 0037452966 scopus 로고    scopus 로고
    • Generalized singular value decomposition for comparative analysis of genomescale expression data sets of two different organisms
    • Alter, O., Brown, P. O., Botstein, D., Generalized singular value decomposition for comparative analysis of genomescale expression data sets of two different organisms. Proc. Natl. Acad. Sci. USA 2003, 100 , 3351-3356.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3351-3356
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 119
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S. et al., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 2005, 102, 15545-15550.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4
  • 121
    • 0038054341 scopus 로고    scopus 로고
    • PGC-1 a-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A. et al., PGC-1 a-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 2003, 34, 267-273.
    • (2003) Nat. Genet , vol.34 , pp. 267-273
    • Mootha, V.K.1    Lindgren, C.M.2    Eriksson, K.F.3    Subramanian, A.4
  • 122
    • 34547483895 scopus 로고    scopus 로고
    • Improving gene set analysis of microarray data by SAM-GS
    • Dinu, I., Potter, J. D., Mueller, T., Liu, Q. et al., Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics 2007, 8, 242.
    • (2007) BMC Bioinformatics , vol.8 , pp. 242
    • Dinu, I.1    Potter, J.D.2    Mueller, T.3    Liu, Q.4
  • 123
    • 0345832338 scopus 로고    scopus 로고
    • A global test for groups of genes: Testing association with a clinical outcome
    • Goeman, J. J., Van de Geer, S. A., De Kort, F., Van Houwelingen, J. C., A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004, 20, 93-99.
    • (2004) Bioinformatics , vol.20 , pp. 93-99
    • Goeman, J.J.1    Van de Geer, S.A.2    De Kort, F.3    Van Houwelingen, J.C.4
  • 124
    • 40549110559 scopus 로고    scopus 로고
    • Protein networking: Insights into global functional organization of proteomes
    • Pieroni, E., de la Fuente van Bentem, S., Mancosu, G., Capobianco, E. et al., Protein networking: insights into global functional organization of proteomes. Proteomics 2008, 8, 799-816.
    • (2008) Proteomics , vol.8 , pp. 799-816
    • Pieroni, E.1    de la Fuente van Bentem, S.2    Mancosu, G.3    Capobianco, E.4
  • 125
    • 36749010218 scopus 로고    scopus 로고
    • The age of crosstalk: Phosphorylation, ubiquitination, and beyond
    • Hunter, T., The age of crosstalk: phosphorylation, ubiquitination, and beyond. Mol. Cell 2007, 28, 730-738.
    • (2007) Mol. Cell , vol.28 , pp. 730-738
    • Hunter, T.1
  • 127
    • 33750351769 scopus 로고    scopus 로고
    • Data-driven modelling of signal-transduction networks
    • Janes, K. A., Yaffe, M. B., Data-driven modelling of signal-transduction networks. Nat. Rev. Mol. Cell. Biol. 2006, 7, 820-828.
    • (2006) Nat. Rev. Mol. Cell. Biol , vol.7 , pp. 820-828
    • Janes, K.A.1    Yaffe, M.B.2
  • 128
    • 34247623628 scopus 로고    scopus 로고
    • Getting connected: Analysis and principles of biological networks
    • Zhu, X., Gerstein, M., Snyder, M., Getting connected: analysis and principles of biological networks. Genes Dev. 2007, 21, 1010-1024.
    • (2007) Genes Dev , vol.21 , pp. 1010-1024
    • Zhu, X.1    Gerstein, M.2    Snyder, M.3
  • 129
    • 0041706161 scopus 로고    scopus 로고
    • Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics
    • Krijgsveld, J., Ketting, R. F., Mahmoudi, T., Johansen, J. et al., Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat. Biotechnol. 2003, 21, 927-931.
    • (2003) Nat. Biotechnol , vol.21 , pp. 927-931
    • Krijgsveld, J.1    Ketting, R.F.2    Mahmoudi, T.3    Johansen, J.4
  • 130
    • 34548391374 scopus 로고    scopus 로고
    • Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development
    • McClatchy, D. B., Liao, L., Park, S. K., Venable, J. D., Yates, J. R., Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development. Genome Res. 2007, 17, 1378-1388.
    • (2007) Genome Res , vol.17 , pp. 1378-1388
    • McClatchy, D.B.1    Liao, L.2    Park, S.K.3    Venable, J.D.4    Yates, J.R.5
  • 131
    • 4444346217 scopus 로고    scopus 로고
    • Wu, C. C., MacCoss, M. J., Howell, K. E., Matthews, D. E., Yates, J. R., 3rd, Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal. Chem. 2004, 76, 4951-4959.
    • Wu, C. C., MacCoss, M. J., Howell, K. E., Matthews, D. E., Yates, J. R., 3rd, Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal. Chem. 2004, 76, 4951-4959.
  • 132
    • 33646899550 scopus 로고    scopus 로고
    • Topdown protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer
    • Macek, B., Waanders, L. F., Olsen, J. V., Mann, M., Topdown protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol. Cell. Proteomics 2006, 5, 949-958.
    • (2006) Mol. Cell. Proteomics , vol.5 , pp. 949-958
    • Macek, B.1    Waanders, L.F.2    Olsen, J.V.3    Mann, M.4
  • 133
    • 35848929694 scopus 로고    scopus 로고
    • Analysis and validation of proteomic data generated by tandem mass spectrometry
    • Nesvizhskii, A. I., Vitek, O., Aebersold, R., Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 2007, 4, 787-797.
    • (2007) Nat. Methods , vol.4 , pp. 787-797
    • Nesvizhskii, A.I.1    Vitek, O.2    Aebersold, R.3
  • 134
    • 34249062964 scopus 로고    scopus 로고
    • The minimum information about a proteomics experiment (MIAPE)
    • Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P. A. et al., The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 2007, 25, 887-893.
    • (2007) Nat. Biotechnol , vol.25 , pp. 887-893
    • Taylor, C.F.1    Paton, N.W.2    Lilley, K.S.3    Binz, P.A.4
  • 135
    • 33846009481 scopus 로고    scopus 로고
    • A phosphoproteomic analysis of the ErbB2 receptor tyrosine kinase signaling pathways
    • Mukherji, M., Brill, L. M., Ficarro, S. B., Hampton, G. M., Schultz, P. G., A phosphoproteomic analysis of the ErbB2 receptor tyrosine kinase signaling pathways. Biochemistry 2006, 45, 15529-15540.
    • (2006) Biochemistry , vol.45 , pp. 15529-15540
    • Mukherji, M.1    Brill, L.M.2    Ficarro, S.B.3    Hampton, G.M.4    Schultz, P.G.5


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