Genomics and Proteomics in Drug Design and Discovery

Pharmacology

Volumn , Issue , 2009, Pages 561-573

  Wang, Ying ^a   Chiu, Jen Fu ^b   He, Qing Yu ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b SHANTOU UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882513776     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-369521-5.00020-8     Document Type: Chapter

References (132)

1. Adam B.L., Vlahou A., Semmes O.J., Wright G.L. Proteomic approaches to biomarker discovery in prostate and bladder cancers. Proteomics 2001, 1:1264-1270.
2. Adam G.C., Burbaum J., Kozarich J.W., Patricelli M.P., Cravatt B.F. Mapping enzyme active sites in complex proteomes. Journal of the American Chemical Society 2004, 126:1363-1368.
3. Adam G.C., Cravatt B.F., Sorensen E.J. Profiling the specific reactivity of the proteome with non-directed activity-based probes. Chemistry & Biology 2001, 8:81-95.
4. Adam G.C., Sorensen E.J., Cravatt B.F. Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype. Nature Biotechnology 2002, 20:805-809.
5. Adam G.C., Sorensen E.J., Cravatt B.F. Trifunctional chemical probes for the consolidated detection and identification of enzyme activities from complex proteomes. Molecular & Cellular Proteomics: MCP 2002, 1:828-835.
6. Adam P.J., Boyd R., Tyson K.L., Fletcher G.C., Stamps A., Hudson L., et al. Comprehensive proteomic analysis of breast cancer cell membranes reveals unique proteins with potential roles in clinical cancer. The Journal of Biological Chemistry 2003, 278:6482-6489.
7. Adkins J.N., Varnum S.M., Auberry K.J., Moore R.J., Angell N.H., Smith R.D., et al. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Molecular & Cellular Proteomics: MCP 2002, 1:947-955.
8. Alonso J.M., Ecker J.R. Moving forward in reverse: Genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nature Reviews. Genetics 2006, 7:524-536.
9. Amaral L.A., Scala A., Barthelemy M., Stanley H.E. Classes of small-world networks. Proceedings of the National Academy of Sciences of the United States of America 2000, 97:11149-11152.
10. An H.J., Kim D.S., Park Y.K., Kim S.K., Choi Y.P., Kang S., et al. Comparative proteomics of ovarian epithelial tumors. Journal of Proteome Research 2006, 5:1082-1090.
11. Anderson N.L., Taylor J., Scandora A.E., Coulter B.P., Anderson N.G. The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns. Clinical Chemistry 1981, 27:1807-1820.
12. Archakov A.I., Govorun V.M., Dubanov A.V., Ivanov Y.D., Veselovsky A.V., Lewi P., Janssen P. Protein-protein interactions as a target for drugs in proteomics. Proteomics 2003, 3:380-391.
13. Arthur J.M. Proteomics. Current Opinion in Nephrology and Hypertension 2003, 12:423-430.
14. Bernstein H., Payne C.M., Kunke K., Crowley-Weber C.L., Waltmire C.N., Dvorakova K., et al. A proteomic study of resistance to deoxycholate-induced apoptosis. Carcinogenesis 2004, 25:681-692.
15. Boyd R.S., Adam P.J., Patel S., Loader J.A., Berry J., Redpath N.T., et al. Proteomic analysis of the cell-surface membrane in chronic lymphocytic leukemia: Identification of two novel proteins, BCNP1 and MIG2B. Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U. K 2003, 17:1605-1612.
16. Braddock M., Quinn A. Targeting IL-1 in inflammatory disease: New opportunities for therapeutic intervention. Nature Reviews. Drug Discovery 2004, 3:330-339.
17. Brehmer D., Greff Z., Godl K., Blencke S., Kurtenbach A., Weber M., et al. Cellular targets of gefitinib. Cancer Research 2005, 65:379-382.
18. Castagna A., Antonioli P., Astner H., Hamdan M., Righetti S.C., Perego P., et al. A proteomic approach to cisplatin resistance in the cervix squamous cell carcinoma cell line A431. Proteomics 2004, 4:3246-3267.
19. Celis J.E., Wolf H., Ostergaard M. Bladder squamous cell carcinoma biomarkers derived from proteomics. Electrophoresis 2000, 21:2115-2121.
20. Chen J., He Q.Y., Yuen A.P., Chiu J.F. Proteomics of buccal squamous cell carcinoma: The involvement of multiple pathways in tumorigenesis. Proteomics 2004, 4:2465-2475.
21. Chen T., Wang Q., Cui J., Yang W., Shi Q., Hua Z., et al. Induction of apoptosis in mouse liver by microcystin-LR: A combined transcriptomic, proteomic, and simulation strategy. Molecular & Cellular Proteomics: MCP 2005, 4:958-974.
22. Cho A., Normile D. Nobel Prize in Chemistry. Mastering macromolecules. Science 2002, 298:527-528.
23. Collins M.O., Yu L., Coba M.P., Husi H., Campuzano I., Blackstock W.P., et al. Proteomic analysis of in vivo phosphorylated synaptic proteins. The Journal of Biological Chemistry 2005, 280:5972-5982.
24. Comunale M.A., Lowman M., Long R.E., Krakover J., Philip R., Seeholzer S., et al. Proteomic analysis of serum associated fucosylated glycoproteins in the development of primary hepatocellular carcinoma. Journal of Proteome Research 2006, 5:308-315.
25. Ding S.J., Li Y., Tan Y.X., Jiang M.R., Tian B., Liu Y.K., et al. From proteomic analysis to clinical significance: Overexpression of cytokeratin 19 correlates with hepatocellular carcinoma metastasis. Molecular & Cellular Proteomics: MCP 2004, 3:73-81.
26. Duggan D.J., Bittner M., Chen Y., Meltzer P., Trent J.M. Expression profiling using cDNA microarrays. Nature Genetics 1999, 21:10-14.
27. Dyment D.A., Ebers G.C. An array of sunshine in multiple sclerosis. The New England Journal of Medicine 2002, 347:1445-1447.
28. Eustace B.K., Sakurai T., Stewart J.K., Yimlamai D., Unger C., Zehetmeier C., et al. Functional proteomic screens reveal an essential extracellular role for hsp90 alpha in cancer cell invasiveness. Nature Cell Biology 2004, 6:507-514.
29. Fenn J.B., Mann M., Meng C.K., Wong S.F., Whitehouse C.M. Electrospray ionization for mass spectrometry of large biomolecules. Science 1989, 246:64-71.
30. Fleming K., Muller A., MacCallum R.M., Sternberg M.J. 3D-GENOMICS: A database to compare structural and functional annotations of proteins between sequenced genomes. Nucleic Acids Research 2004, 32:D245-D250.
31. Girvan M., Newman M.E. Community structure in social and biological networks. Proceedings of the National Academy of Sciences of the United States of America 2002, 99:7821-7826.
32. Godl K., Wissing J., Kurtenbach A., Habenberger P., Blencke S., Gutbrod H., et al. An efficient proteomics method to identify the cellular targets of protein kinase inhibitors. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:15434-15439.
33. Goffeau A., Barrell B.G., Bussey H., Davis R.W., Dujon B., Feldmann H., et al. Life with 6000 genes. Science 1996, 274:546. 563-566, 567.
34. Graves P.R., Kwiek J.J., Fadden P., Ray R., Hardeman K., Coley A.M., et al. Discovery of novel targets of quinoline drugs in the human purine binding proteome. Molecular Pharmacology 2002, 62:1364-1372.
35. Grossman H.B., Soloway M., Messing E., Katz G., Stein B., Kassabian V., et al. Surveillance for recurrent bladder cancer using a point-of-care proteomic assay. JAMA: The Journal of the American Medical Association 2006, 295:299-305.
36. Gu S., Du Y., Chen J., Liu Z., Bradbury E.M., Hu C.A., Chen X. Large-scale quantitative proteomic study of PUMA-induced apoptosis using two-dimensional liquid chromatography-mass spectrometry coupled with amino acid-coded mass tagging. Journal of Proteome Research 2004, 3:1191-1200.
37. Hanash S. Disease proteomics. Nature 2003, 422:226-232.
38. He Q.Y., Chen J., Kung H.F., Yuen A.P., Chiu J.F. Identification of tumor-associated proteins in oral tongue squamous cell carcinoma by proteomics. Proteomics 2004, 4:271-278.
39. He Q.Y., Chiu J.F. Proteomics in biomarker discovery and drug development. Journal of Cellular Biochemistry 2003, 89:868-886.
40. He Q.Y., Lau G.K., Zhou Y., Yuen S.T., Lin M.C., Kung H.F., et al. Serum biomarkers of hepatitis B virus infected liver inflammation: A proteomic study. Proteomics 2003, 3:666-674.
41. Heine G., Raida M., Forssmann W.G. Mapping of peptides and protein fragments in human urine using liquid chromatography-mass spectrometry. Journal of Chromatography. A 1997, 776:117-124.
42. Hock D., Magerlein M., Heine G., Ochlich P.P., Forssmann W.G. Isolation and characterization of the bioactive circulating human parathyroid hormone, hPTH-1-37. FEBS Letters 1997, 400:221-225.
43. Hu W., Wu W., Verschraegen C.F., Chen L., Mao L., Yeung S.C., et al. Proteomic identification of heat shock protein 70 as a candidate target for enhancing apoptosis induced by farnesyl transferase inhibitor. Proteomics 2003, 3:1904-1911.
44. Hughes D. Exploiting genomics, genetics and chemistry to combat antibiotic resistance. Nature Reviews. Genetics 2003, 4:432-441.
45. Humphery-Smith I., Cordwell S.J., Blackstock W.P. Proteome research: Complementarity and limitations with respect to the RNA and DNA worlds. Electrophoresis 1997, 18:1217-1242.
46. Imamura T., Kanai F., Kawakami T., Amarsanaa J., Ijichi H., Hoshida Y., et al. Proteomic analysis of the TGF-beta signaling pathway in pancreatic carcinoma cells using stable RNA interference to silence Smad4 expression. Biochemical and Biophysical Research Communications 2004, 318:289-296.
47. Jacobs I.J., Menon U. Progress and challenges in screening for early detection of ovarian cancer. Molecular & Cellular Proteomics: MCP 2004, 3:355-366.
48. Jeffery D.A., Bogyo M. Chemical proteomics and its application to drug discovery. Current Opinion in Biotechnology 2003, 14:87-95.
49. Jensen O.N. Interpreting the protein language using proteomics. Nature Reviews. Molecular Cell Biology 2006, 7:391-403.
50. Jin K., Mao X.O., Cottrell B., Schilling B., Xie L., Row R.H., et al. Proteomic and immunochemical characterization of a role for stathmin in adult neurogenesis. The FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology 2004, 18:287-299.
51. Jordan M.A., Wilson L. Microtubules and actin filaments: Dynamic targets for cancer chemotherapy. Current Opinion in Cell Biology 1998, 10:123-130.
52. Jung J.W., Jung S.H., Kim H.S., Yuk J.S., Park J.B., Kim Y.M., et al. High-throughput analysis of GST-fusion protein expression and activity-dependent protein interactions on GST-fusion protein arrays with a spectral surface plasmon resonance biosensor. Proteomics 2006, 6:1110-1120.
53. Kageyama S., Isono T., Iwaki H., Wakabayashi Y., Okada Y., Kontani K., et al. Identification by proteomic analysis of calreticulin as a marker for bladder cancer and evaluation of the diagnostic accuracy of its detection in urine. Clinical Chemistry 2004, 50:857-866.
54. Kamath R.S., Fraser A.G., Dong Y., Poulin G., Durbin R., Gotta M., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003, 421:231-237.
55. Karas M., Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Analytical Chemistry 1988, 60:2299-2301.
56. Kebarle P. A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry. Journal of Mass Spectrometry: JMS 2000, 35:804-817.
57. Khawaja X., Xu J., Liang J.J., Barrett J.E. Proteomic analysis of protein changes developing in rat hippocampus after chronic antidepressant treatment: Implications for depressive disorders and future therapies. Journal of Neuroscience Research 2004, 75:451-460.
58. Kopec K.K., Bozyczko-Coyne D., Williams M. Target identification and validation in drug discovery: The role of proteomics. Biochemical Pharmacology 2005, 69:1133-1139.
59. Kopf E., Shnitzer D., Zharhary D. Panorama Ab Microarray Cell Signaling kit: a unique tool for protein expression analysis. Proteomics 2005, 5:2412-2416.
60. Kramer R., Cohen D. Functional genomics to new drug targets. Nature Reviews. Drug Discovery 2004, 3:965-972.
61. Kumar J.K., Tabor S., Richardson C.C. Proteomic analysis of thioredoxin-targeted proteins in Escherichia coli. Proc Natl Acad Sci USA 2004, 101:3759-3764.
62. Kulms D., Dussmann H., Poppelmann B., Stander S., Schwarz A., Schwarz T. Apoptosis induced by disruption of the actin cytoskeleton is mediated via activation of CD95 (Fas/APO-1). Cell Death and Differentiation 2002, 9:598-608.
63. Labugger R., McDonough J.L., Neverova I., Van Eyk J.E. Solubilization, two-dimensional separation and detection of the cardiac myofilament protein troponin T. Proteomics 2002, 2:673-678.
64. Lau A.T., He Q.Y., Chiu J.F. A proteome analysis of the arsenite response in cultured lung cells: Evidence for in vitro oxidative stress-induced apoptosis. The Biochemical Journal 2004, 382:641-650.
65. Li N., Guo R., Li W., Shao J., Li S., Zhao K., et al. A proteomic investigation into a human gastric cancer cell line BGC823 treated with diallyl trisulfide. Carcinogenesis 2005.
66. Liao E.H., Hung W., Abrams B., Zhen M. An SCF-like ubiquitin ligase complex that controls presynaptic differentiation. Nature 2004, 430:345-350.
67. Linding R., Jensen L.J., Diella F., Bork P., Gibson T.J., Russell R.B. Protein disorder prediction: implications for structural proteomics. Structure (Camb.) 2003, 11:1453-1459.
68. Liu Y., Patricelli M.P., Cravatt B.F. Activity-based protein profiling: The serine hydrolases. Proceedings of the National Academy of Sciences of the United States of America 1999, 96:14694-14699.
69. Lockhart D.J., Dong H., Byrne M.C., Follettie M.T., Gallo M.V., Chee M.S., et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 1996, 14:1675-1680.
70. Longley D.B., Johnston P.G. Molecular mechanisms of drug resistance. The Journal of Pathology 2005, 205:275-292.
71. Luker K.E., Smith M.C., Luker G.D., Gammon S.T., Piwnica-Worms H., Piwnica-Worms D. Kinetics of regulated protein-protein interactions revealed with firefly luciferase complementation imaging in cells and living animals. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:12288-12293.
72. MacKeigan J.P., Clements C.M., Lich J.D., Pope R.M., Hod Y., Ting J.P. Proteomic profiling drug-induced apoptosis in non-small cell lung carcinoma: Identification of RS/DJ-1 and RhoGDIalpha. Cancer Research 2003, 63:6928-6934.
73. Maggio E.T., Ramnarayan K. Recent developments in computational proteomics. Drug Discovery Today 2001, 6:996-1004.
74. Mayr M., Zhang J., Greene A.S., Gutterman D.D., Perloff J.K., Ping P. Proteomic based development of biomarkers in cardiovascular disease: Mechanistic, clinical, and therapeutic insights. Molecular & Cellular Proteomics: MCP 2006.
75. Montaudo M.S. Mass spectra of copolymers. Mass Spectrometry Reviews 2002, 21:108-144.
76. Mullis K., Faloona F., Scharf S., Saiki R., Horn G., Erlich H. Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction. Cold Spring Harbor Symposia on Quantitative Biology 1986, 51(Pt 1):263-273.
77. Nawrocki S.T., Carew J.S., Pino M.S., Highshaw R.A., Dunner K., Huang P., et al. Bortezomib sensitizes pancreatic cancer cells to endoplasmic reticulum stress-mediated apoptosis. Cancer Research 2005, 65:11658-11666.
78. Nielsen U.B., Cardone M.H., Sinskey A.J., MacBeath G., Sorger P.K. Profiling receptor tyrosine kinase activation by using Ab microarrays. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:9330-9335.
79. Niture S.K., Doneanu C.E., Velu C.S., Bailey N.I., Srivenugopal K.S. Proteomic analysis of human O6-methylguanine-DNA methyltransferase by affinity chromatography and tandem mass spectrometry. Biochemical and Biophysical Research Communications 2005, 337:1176-1184.
80. Norell H., Carlsten M., Ohlum T., Malmberg K.J., Masucci G., Schedvins K., et al. Frequent loss of HLA-A2 expression in metastasizing ovarian carcinomas associated with genomic haplotype loss and HLA-A2-restricted HER-2/neu-specific immunity. Cancer Research 2006, 66:6387-6394.
81. O'Farrell P.H. High resolution two-dimensional electrophoresis of proteins. The Journal of Biological Chemistry 1975, 250:4007-4021.
82. O'Neill E., Rushworth L., Baccarini M., Kolch W. Role of the kinase MST2 in suppression of apoptosis by the proto-oncogene product Raf-1. Science 2004, 306:2267-2270.
83. Okada M., Itoh H., Hatakeyama T., Tokumitsu H., Kobayashi R. Hsp90 is a direct target of the anti-allergic drugs disodium cromoglycate and amlexanox. The Biochemical Journal 2003, 374:433-441.
84. Paradis V., Degos F., Dargere D., Pham N., Belghiti J., Degott C., et al. Identification of a new marker of hepatocellular carcinoma by serum protein profiling of patients with chronic liver diseases. Hepatology (Baltimore, Md.) 2005, 41:40-47.
85. Park K.S., Kim H., Kim N.G., Cho S.Y., Choi K.H., Seong J.K., et al. Proteomic analysis and molecular characterization of tissue ferritin light chain in hepatocellular carcinoma. Hepatology (Baltimore, Md.) 2002, 35:1459-1466.
86. Petricoin E.F., Ardekani A.M., Hitt B.A., Levine P.J., Fusaro V.A., Steinberg S.M., et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002, 359:572-577.
87. Petricoin E.F., Ornstein D.K., Liotta L.A. Clinical proteomics: Applications for prostate cancer biomarker discovery and detection. Urologic Oncology 2004, 22:322-328.
88. Pinet F., Poirier F., Fuchs S., Tharaux P.L., Caron M., Corvol P., et al. Troponin T as a marker of differentiation revealed by proteomic analysis in renal arterioles. The FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology 2004, 18:585-586.
89. Qiao J., Kang J., Cree J., Evers B.M., Chung D.H. Gastrin-releasing peptide-induced down-regulation of tumor suppressor protein PTEN (phosphatase and tensin homolog deleted on chromosome ten) in neuroblastomas. Annals of Surgery 2005, 241:684-691.
90. Rai A.J., Chan D.W. Cancer proteomics: Serum diagnostics for tumor marker discovery. Annals of the New York Academy of Sciences 2004, 1022:286-294.
91. Renfrey S., Featherstone J. Structural proteomics. Nature Reviews. Drug Discovery 2002, 1:175-176.
92. Reyzer M.L., Caldwell R.L., Dugger T.C., Forbes J.T., Ritter C.A., Guix M., et al. Early changes in protein expression detected by mass spectrometry predict tumor response to molecular therapeutics. Cancer Research 2004, 64:9093-9100.
93. Righetti P.G., Castagna A., Antonioli P., Boschetti E. Prefractionation techniques in proteome analysis: The mining tools of the third millennium. Electrophoresis 2005, 26:297-319.
94. Rodriguez M., Li S.S., Harper J.W., Songyang Z. An oriented peptide array library (OPAL) strategy to study protein-protein interactions. The Journal of Biological Chemistry 2004, 279:8802-8807.
95. Rosamond J., Allsop A. Harnessing the power of the genome in the search for new antibiotics. Science 2000, 287:1973-1976.
96. Sali A., Glaeser R., Earnest T., Baumeister W. From words to literature in structural proteomics. Nature 2003, 422:216-225.
97. Sanishvili R., Yakunin A.F., Laskowski R.A., Skarina T., Evdokimova E., Doherty-Kirby A., et al. Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. The Journal of Biological Chemistry 2003, 278:26039-26045.
98. Sauer S., Lange B.M., Gobom J., Nyarsik L., Seitz H., Lehrach H. Miniaturization in functional genomics and proteomics. Nature Reviews. Genetics 2005, 6:465-476.
99. Schena M., Shalon D., Davis R.W., Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470.
100. Schubert W. Topological proteomics, toponomics, MELK-technology. Advances in Biochemical Engineering/Biotechnology 2003, 83:189-209.
101. Serebriiskii I.G., Mitina O., Pugacheva E.N., Benevolenskaya E., Kotova E., Toby G.G., et al. Detection of peptides, proteins, and drugs that selectively interact with protein targets. Genome Research 2002, 12:1785-1791.
102. Shiio Y., Suh K.S., Lee H., Yuspa S.H., Eisenman R.N., Aebersold R. Quantitative proteomic analysis of myc-induced apoptosis: a direct role for Myc induction of the mitochondrial chloride ion channel, mtCLIC/CLIC4. The Journal of Biological Chemistry 2006, 281:2750-2756.
103. Sielaff I., Arnold A., Godin G., Tugulu S., Klok H.A., Johnsson K. Protein function microarrays based on self-immobilizing and self-labeling fusion proteins. Chembiochem: A European Journal of Chemical Biology 2006, 7:194-202.
104. Sitek B., Apostolov O., Stuhler K., Pfeiffer K., Meyer H.E., Eggert A., et al. Identification of dynamic proteome changes upon ligand activation of Trk-receptors using two-dimensional fluorescence difference gel electrophoresis and mass spectrometry. Molecular & Cellular Proteomics: MCP 2005, 4:291-299.
105. Skalnikova H., Halada P., Dzubak P., Hajduch M., Kovarova H. Protein fingerprints of anti-cancer effects of cyclin-dependent kinase inhibition: Identification of candidate biomarkers using 2-D liquid phase separation coupled to mass spectrometry. Technology in Cancer Research & Treatment 2005, 4:447-454.
106. Song K.H., An H.M., Kim H.J., Ahn S.H., Chung S.J., Shim C.K. Simple liquid chromatography-electrospray ionization mass spectrometry method for the routine determination of salmon calcitonin in serum. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences 2002, 775:247-255.
107. Stasyk T., Huber L.A. Zooming in: Fractionation strategies in proteomics. Proteomics 2004, 4:3704-3716.
108. Stoughton R.B., Friend S.H. How molecular profiling could revolutionize drug discovery. Nature Reviews. Drug Discovery 2005, 4:345-350.
109. Sun X., Chiu J.F., He Q.Y. Application of immobilized metal affinity chromatography in proteomics. Expert Reviews of Proteomics 2005, 2:649-657.
110. Takashima M., Kuramitsu Y., Yokoyama Y., Iizuka N., Fujimoto M., Nishisaka T., et al. Overexpression of alpha enolase in hepatitis C virus-related hepatocellular carcinoma: Association with tumor progression as determined by proteomic analysis. Proteomics 2005, 5:1686-1692.
111. Takashima M., Kuramitsu Y., Yokoyama Y., Iizuka N., Toda T., Sakaida I., et al. Proteomic profiling of heat shock protein 70 family members as biomarkers for hepatitis C virus-related hepatocellular carcinoma. Proteomics 2003, 3:2487-2493.
112. Towbin H., Bair K.W., DeCaprio J.A., Eck M.J., Kim S., Kinder F.R., et al. Proteomics-based target identification: Bengamides as a new class of methionine aminopeptidase inhibitors. The Journal of Biological Chemistry 2003, 278:52964-52971.
113. Valianpour F., Wanders R.J., Barth P.G., Overmars H., van Gennip A.H. Quantitative and compositional study of cardiolipin in platelets by electrospray ionization mass spectrometry: Application for the identification of Barth syndrome patients. Clinical Chemistry 2002, 48:1390-1397.
114. Vaux D.L., Korsmeyer S.J. Cell death in development. Cell 1999, 96:245-254.
115. Venkatraman A., Landar A., Davis A.J., Chamlee L., Sanderson T., Kim H., et al. Modification of the mitochondrial proteome in response to the stress of ethanol-dependent hepatotoxicity. The Journal of Biological Chemistry 2004, 279:22092-22101.
116. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., et al. The sequence of the human genome. Science 2001, 291:1304-1351.
117. Verrills N.M., Walsh B.J., Cobon G.S., Hains P.G., Kavallaris M. Proteome analysis of vinca alkaloid response and resistance in acute lymphoblastic leukemia reveals novel cytoskeletal alterations. The Journal of Biological Chemistry 2003, 278:45082-45093.
118. Vivanco F., Martin-Ventura J.L., Duran M.C., Barderas M.G., Blanco-Colio L., Darde V.M., et al. Quest for novel cardiovascular biomarkers by proteomic analysis. Journal of Proteome Research 2005, 4:1181-1191.
119. Wang Y., He Q.Y., Sun R.W., Che C.M., Chiu J.F. Gold(III) Porphyrin 1a induced apoptosis by mitochondrial death pathways related to reactive oxygen species. Cancer Research 2005, 65:11553-11564.
120. Wang Y., Cheung Y.H., Yang Z., Chiu J.F., Che C.M., He Q.Y. Proteomic approach to study the cytotoxicity of dioscin (saponin). Proteomics 2006, 6:2422-2432.
121. Wang Y., Hanley R., Klemke R.L. Computational methods for comparison of large genomic and proteomic datasets reveal protein markers of metastatic cancer. Journal of Proteome Research 2006, 5:907-915.
122. Wang Y., He Q.Y., Che C.M., Chiu J.F. Proteomic characterization of the cytotoxic mechanism of gold (III) porphyrin 1a, a potential anticancer drug. Proteomics 2006, 6:131-142.
123. Wasinger V.C., Cordwell S.J., Cerpa-Poljak A., Yan J.X., Gooley A.A., Wilkins M.R., et al. Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 1995, 16:1090-1094.
124. Watson J.D. The human genome project: Past, present, and future. Science 1990, 248:44-49.
125. Whitehouse C.M., Dreyer R.N., Yamashita M., Fenn J.B. Electrospray interface for liquid chromatographs and mass spectrometers. Analytical Chemistry 1985, 57:675-679.
126. Yamazaki Y., Tsuruga M., Zhou D., Fujita Y., Shang X., Dang Y., et al. Cytoskeletal disruption accelerates caspase-3 activation and alters the intracellular membrane reorganization in DNA damage-induced apoptosis. Experimental Cell Research 2000, 259:64-78.
127. Yan Y., Weaver V.M., Blair I.A. Analysis of protein expression during oxidative stress in breast epithelial cells using a stable isotope labeled proteome internal standard. Journal of Proteome Research 2005, 4:2007-2014.
128. Yates J.R. Mass spectrometry and the age of the proteome. Journal of Mass Spectrometry: JMS 1998, 33:1-19.
129. Yim E.K., Lee K.H., Bae J.S., Namkoong S.E., Um S.J., Park J.S. Proteomic analysis of antiproliferative effects by treatment of 5-fluorouracil in cervical cancer cells. DNA and Cell Biology 2004, 23:769-776.
130. Yu H., Zhu X., Greenbaum D., Karro J., Gerstein M. TopNet: A tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Research 2004, 32:328-337.
131. Zeindl-Eberhart E., Haraida S., Liebmann S., Jungblut P.R., Lamer S., Mayer D., et al. Detection and identification of tumor-associated protein variants in human hepatocellular carcinomas. Hepatology (Baltimore, Md.) 2004, 39:540-549.
132. Zhu W., Wang X., Ma Y., Rao M., Glimm J., Kovach J.S. Detection of cancer-specific markers amid massive mass spectral data. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:14666-14671.