Systems Biology and Systems Medicine

Essentials of Genomic and Personalized Medicine

Volumn , Issue , 2010, Pages 131-141

  Price, Nathan D ^b   Edelman, Lucas B ^b   Lee, Inyoul ^b   Yoo, Hyuntae ^b   Hwang, Daehee ^b   Carlson, George ^b   Galas, David J ^b   Heath, James R ^b   Hood, Leroy ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882756248     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-374934-5.00011-8     Document Type: Chapter

References (82)

1. Adler A.S., Chang H.Y. From description to causality: Mechanisms of gene expression signatures in cancer. Cell Cycle 2006, 5:1148-1151.
2. Anderson N.L., Anderson N.G. The human plasma proteome: History, character, and diagnostic prospects. Mol Cell Proteomics 2002, 1:845-867.
3. Bailey R.C., Kwong G.A., Radu C.G., Witte O.N., Heath J.R. DNA-encoded antibody libraries: A unified platform for multiplexed cell sorting and detection of genes and proteins. J Am Chem Soc 2007, 129:1959-1967.
4. Barrier A., Boelle P.Y., Roser F., Gregg J., Tse C., Brault D., Lacaine F., Houry S., Huguier M., Franc B., et al. Stage II colon cancer prognosis prediction by tumor gene expression profiling. J Clin Oncol 2006, 24:4685-4691.
5. Buttner P., Mosig S., Lechtermann A., Funke H., Mooren F.C. Exercise affects the gene expression profiles of human white blood cells. J Appl Physiol 2007, 102:26-36.
6. Buyse M., Loi S., van't Veer L., Viale G., Delorenzi M., Glas A.M., d'Assignies M.S., Bergh J., Lidereau R., Ellis P., et al. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 2006, 98:1183-1192.
7. Czernin J., Phelps M.E. Positron emission tomography scanning: Current and future applications. Annu Rev Med 2002, 53:89-112.
8. Dai H., van't Veer L., Lamb J., He Y.D., Mao M., Fine B.M., Bernards R., van de Vijver M., Deutsch P., Sachs A., et al. A cell proliferation signature is a marker of extremely poor outcome in a subpopulation of breast cancer patients. Cancer Res 2005, 65:4059-4066.
9. De Cecco L., Marchionni L., Gariboldi M., Reid J.F., Lagonigro M.S., Caramuta S., Ferrario C., Bussani E., Mezzanzanica D., Turatti F., et al. Gene expression profiling of advanced ovarian cancer: Characterization of a molecular signature involving fibroblast growth factor 2. Oncogene 2004, 23:8171-8183.
10. Dhanasekaran S.M., Barrette T.R., Ghosh D., Shah R., Varambally S., Kurachi K., Pienta K.J., Rubin M.A., Chinnaiyan A.M. Delineation of prognostic biomarkers in prostate cancer. Nature 2001, 412:822-826.
11. Duarte N.C., Becker S.A., Jamshidi N., Thiele I., Mo M.L., Vo T.D., Srivas R., Palsson B.O. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci USA 2007, 104:1777-1782.
12. Dupuy A., Simon R.M. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 2007, 99:147-157.
13. Foekens J.A., Atkins D., Zhang Y., Sweep F.C., Harbeck N., Paradiso A., Cufer T., Sieuwerts A.M., Talantov D., Span P.N., et al. Multicenter validation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer. J Clin Oncol 2006, 24:1665-1671.
14. Fujii K., Nakano T., Kawamura T., Usui F., Bando Y., Wang R., Nishimura T. Multidimensional protein profiling technology and its application to human plasma proteome. J Proteome Res 2004, 3:712-718.
15. Fuller G.N., Mircean C., Tabus I., Taylor E., Sawaya R., Bruner J.M., Shmulevich I., Zhang W. Molecular voting for glioma classification reflecting heterogeneity in the continuum of cancer progression. Oncol Rep 2005, 14:651-656.
16. Furey T.S., Cristianini N., Duffy N., Bednarski D.W., Schummer M., Haussler D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 2000, 16:906-914.
17. Gao W.M., Kuick R., Orchekowski R.P., Misek D.E., Qiu J., Greenberg A.K., Rom W.N., Brenner D.E., Omenn G.S., Haab B.B., et al. Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis. BMC Cancer 2005, 5:110.
18. Geman D., d'Avignon C., Naiman D.Q., Winslow R.L. Classifying gene expression profiles from pairwise mRNA comparisons. Stat Appl Genet Mol Biol 2004, 3(Article19).
19. Giacomini C.P., Leung S.Y., Chen X., Yuen S.T., Kim Y.H., Bair E., Pollack J.R. A gene expression signature of genetic instability in colon cancer. Cancer Res 2005, 65:9200-9205.
20. Glinsky G.V., Glinskii A.B., Stephenson A.J., Hoffman R.M., Gerald W.L. Gene expression profiling predicts clinical outcome of prostate cancer. J Clin Invest 2004, 113:913-923.
21. Glinsky G.V., Higashiyama T., Glinskii A.B. Classification of human breast cancer using gene expression profiling as a component of the survival predictor algorithm. Clin Cancer Res 2004, 10:2272-2283.
22. Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A., et al. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
23. Goncalves A., Esterni B., Bertucci F., Sauvan R., Chabannon C., Cubizolles M., Bardou V.J., Houvenaegel G., Jacquemier J., Granjeaud S., et al. Postoperative serum proteomic profiles may predict metastatic relapse in high-risk primary breast cancer patients receiving adjuvant chemotherapy. Oncogene 2006, 25:981-989.
24. Haab B.B., Dunham M.J., Brown P.O. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol 2001, 2. RESEARCH0004.
25. Halvorsen O.J., Oyan A.M., Bo T.H., Olsen S., Rostad K., Haukaas S.A., Bakke A.M., Marzolf B., Dimitrov K., Stordrange L., et al. Gene expression profiles in prostate cancer: Association with patient subgroups and tumour differentiation. Int J Oncol 2005, 26:329-336.
26. Hood L., Heath J.R., Phelps M.E., Lin B. Systems biology and new technologies enable predictive and preventative medicine. Science 2004, 306:640-643.
27. Hu, Z., Hood, L. and Tian, Q. (2007). Quantitative proteomic approaches for biomarker discovery. Proteomics. In review.
28. Huber W., Mueller F. Biomolecular interaction analysis in drug discovery using surface plasmon resonance technology. Curr Pharm Des 2006, 12:3999-4021.
29. Ito T., Chiba T., Ozawa R., Yoshida M., Hattori M., Sakaki Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2001, 98:4569-4574.
30. Ivshina A.V., George J., Senko O., Mow B., Putti T.C., Smeds J., Lindahl T., Pawitan Y., Hall P., Nordgren H., et al. Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res 2006, 66:10292-10301.
31. Joshi-Tope G., Gillespie M., Vastrik I., D'Eustachio P., Schmidt E., de Bono B., Jassal B., Gopinath G.R., Wu G.R., Matthews L., et al. Reactome: A knowledgebase of biological pathways. Nucleic Acids Res 2005, 33:D428-D432.
32. Kim S., Dougherty E.R., Shmulevich I., Hess K.R., Hamilton S.R., Trent J.M., Fuller G.N., Zhang W. Identification of combination gene sets for glioma classification. Mol Cancer Ther 2002, 1:1229-1236.
33. Koga H., Kyo M., Usui-Aoki K., Inamori K. A chip-based miniaturized format for protein-expression profiling: the exploitation of comprehensively produced antibodies. Electrophoresis 2006, 27:3676-3683.
34. Lathrop J.T., Anderson N.L., Anderson N.G., Hammond D.J. Therapeutic potential of the plasma proteome. Curr Opin Mol Ther 2003, 5:250-257.
35. Lee H.J., Lee E.Y., Kwon M.S., Paik Y.K. Biomarker discovery from the plasma proteome using multidimensional fractionation proteomics. Curr Opin Chem Biol 2006, 10:42-49.
36. Lin B., White J.T., Lu W., Xie T., Utleg A.G., Yan X., Yi E.C., Shannon P., Khrebtukova I., Lange P.H., et al. Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: A systems approach to disease. Cancer Res 2005, 65:3081-3091.
37. Liu R., Wang X., Chen G.Y., Dalerba P., Gurney A., Hoey T., Sherlock G., Lewicki J., Shedden K., Clarke M.F. The prognostic role of a gene signature from tumorigenic breast- cancer cells. N Engl J Med 2007, 356:217-226.
38. Luo J., Dunn T., Ewing C., Sauvageot J., Chen Y., Trent J., Isaacs W. Gene expression signature of benign prostatic hyperplasia revealed by cDNA microarray analysis. Prostate 2002, 51:189-200.
39. Lyon L.A., Musick M.D., Natan M.J. Colloidal Au-enhanced surface plasmon resonance immunosensing. Anal Chem 1998, 70:5177-5183.
40. Ma X.J., Wang Z., Ryan P.D., Isakoff S.J., Barmettler A., Fuller A., Muir B., Mohapatra G., Salunga R., Tuggle J.T., et al. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004, 5:607-616.
41. Miller J.C., Zhou H., Kwekel J., Cavallo R., Burke J., Butler E.B., Teh B.S., Haab B.B. Antibody microarray profiling of human prostate cancer sera: Antibody screening and identification of potential biomarkers. Proteomics 2003, 3:56-63.
42. Mulquiney P.J., Kuchel P.W. Modelling metabolism with Mathematica Detailed Examples Including Erythrocyte Metabolism 2003, CRC Press, Boca Raton, Fla.
43. Nuyten D.S., Kreike B., Hart A.A., Chi J.T., Sneddon J.B., Wessels L.F., Peterse H.J., Bartelink H., Brown P.O., Chang H.Y., et al. Predicting a local recurrence after breast-conserving therapy by gene expression profiling. Breast Cancer Res 2006, 8:R62.
44. Olle E.W., Sreekumar A., Warner R.L., McClintock S.D., Chinnaiyan A.M., Bleavins M.R., Anderson T.D., Johnson K.J. Development of an internally controlled antibody microarray. Mol Cell Proteomics 2005, 4:1664-1672.
45. Orchekowski R., Hamelinck D., Li L., Gliwa E., vanBrocklin M., Marrero J.A., Vande Woude G.F., Feng Z., Brand R., Haab B.B. Antibody microarray profiling reveals individual and combined serum proteins associated with pancreatic cancer. Cancer Res 2005, 65:11193-11202.
46. Palsson B. Two-dimensional annotation of genomes. Nat Biotechnol 2004, 22:1218-1219.
47. Papadopoulou E., Davilas E., Sotiriou V., Georgakopoulos E., Georgakopoulou S., Koliopanos A., Aggelakis F., Dardoufas K., Agnanti N.J., Karydas I., et al. Cell-free DNA and RNA in plasma as a new molecular marker for prostate and breast cancer. Ann N Y Acad Sci 2006, 1075:235-243.
48. Park E.S., Lee J.S., Woo H.G., Zhan F., Shih J.H., Shaughnessy J.D., Frederic Mushinski J. Heterologous tissue culture expression signature predicts human breast cancer prognosis. PLoS ONE 2007, 2:e145.
49. Pawitan Y., Bjohle J., Amler L., Borg A.L., Egyhazi S., Hall P., Han X., Holmberg L., Huang F., Klaar S., et al. Gene expression profiling spares early breast cancer patients from adjuvant therapy: Derived and validated in two population-based cohorts. Breast Cancer Res 2005, 7:R953-R964.
50. Price N.D., Shmulevich I. Biochemical and statistical network models for systems biology. Curr Opin Biotechnol 2007, 18:365-370.
51. Price N.D., Reed J.L., Palsson B.O. Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat Rev Microbiol 2004, 2:886-897.
52. Price N.D., Schellenberger J., Palsson B.O. Uniform sampling of steady-state flux spaces: Means to design experiments and to interpret enzymopathies. Biophys J 2004, 87:2172-2186.
53. Price N.D., Trent J., El-Naggar A.K., Cogdell D., Taylor E., Hunt K.K., Pollock R.E., Hood L., Shmulevich I., Zhang W. Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci USA 2007, 104:3414-3419.
54. Quackenbush J. Microarray analysis and tumor classification. N Engl J Med 2006, 354:2463-2472.
55. Ramaswamy S., Tamayo P., Rifkin R., Mukherjee S., Yeang C.H., Angelo M., Ladd C., Reich M., Latulippe E., Mesirov J.P. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 2001, 98:15149-15154.
56. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., Khainovski N., Pillai S., Dey S., Daniels S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
57. Ruvkun G. Molecular biology. Glimpses of a tiny RNA world. Science 2001, 294:797-799.
58. Sanchez-Carbayo M., Socci N.D., Lozano J.J., Haab B.B., Cordon-Cardo C. Profiling bladder cancer using targeted antibody arrays. Am J Pathol 2006, 168:93-103.
59. Scherzer C.R., Eklund A.C., Morse L.J., Liao Z., Locascio J.J., Fefer D., Schwarzschild M.A., Schlossmacher M.G., Hauser M.A., Vance J.M., et al. Molecular markers of early Parkinson's disease based on gene expression in blood. Proc Natl Acad Sci USA 2007, 104:955-960.
60. Simon R. Roadmap for developing and validating therapeutically relevant genomic classifiers. J Clin Oncol 2005, 23:7332-7341.
61. Singh D., Febbo P.G., Ross K., Jackson D.G., Manola J., Ladd C., Tamayo P., Renshaw A.A., D'Amico A.V., Richie J.P., et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 2002, 1:203-209.
62. Smith D.I. Transcriptional profiling develops molecular signatures for ovarian tumors. Cytometry 2002, 47:60-62.
63. Solanky K.S., Bailey N.J., Beckwith-Hall B.M., Davis A., Bingham S., Holmes E., Nicholson J.K., Cassidy A. Application of biofluid 1H nuclear magnetic resonance-based metabonomic techniques for the analysis of the biochemical effects of dietary isoflavones on human plasma profile. Anal Biochem 2003, 323:197-204.
64. Song S., Li B., Wang L., Wu H., Hu J., Li M., Fan C. A cancer protein microarray platform using antibody fragments and its clinical applications. Mol Biosyst 2007, 3:151-158.
65. Spentzos D., Levine D.A., Ramoni M.F., Joseph M., Gu X., Boyd J., Libermann T.A., Cannistra S.A. Gene expression signature with independent prognostic significance in epithelial ovarian cancer. J Clin Oncol 2004, 22:4700-4710.
66. Stark C., Breitkreutz B.J., Reguly T., Boucher L., Breitkreutz A., Tyers M. BioGRID: A general repository for interaction datasets. Nucleic Acids Res 2006, 34:D535-D539.
67. Sun B., Ranish J.A., Utleg A.G., White J.T., Yan X., Lin B., Hood L. Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics. Mol Cell Proteomics 2007, 6:141-149.
68. Tan A.C., Naiman D.Q., Xu L., Winslow R.L., Geman D. Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics 2005, 21:3896-3904.
69. Thiele I., Price N.D., Vo T.D., Palsson B.O. Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem 2005, 280:11683-11695.
70. Thomassen M., Tan Q., Eiriksdottir F., Bak M., Cold S., Kruse T.A. Prediction of metastasis from low-malignant breast cancer by gene expression profiling. Int J Cancer 2007, 120:1070-1075.
71. Usui-Aoki K., Shimada K., Nagano M., Kawai M., Koga H. A novel approach to protein expression profiling using antibody microarrays combined with surface plasmon resonance technology. Proteomics 2005, 5:2396-2401.
72. van 't Veer L.J., Dai H., van de Vijver M.J., He Y.D., Hart A.A., Mao M., Peterse H.L., van der Kooy K., Marton M.J., Witteveen A.T., et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536.
73. van de Vijver M.J., He Y.D., van't Veer L.J., Dai H., Hart A.A., Voskuil D.W., Schreiber G.J., Peterse J.L., Roberts C., Marton M.J., et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002, 347:1999-2009.
74. Wang X., Yu J., Sreekumar A., Varambally S., Shen R., Giacherio D., Mehra R., Montie J.E., Pienta K.J., Sanda M.G., et al. Autoantibody signatures in prostate cancer. N Engl J Med 2005, 353:1224-1235.
75. Wang Y., Klijn J.G., Zhang Y., Sieuwerts A.M., Look M.P., Yang F., Talantov D., Timmermans M., Meijer-van Gelder M.E., Yu J., et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005, 365:671-679.
76. Weigelt B., Hu Z., He X., Livasy C., Carey L.A., Ewend M.G., Glas A.M., Perou C.M., Van't Veer L.J. Molecular portraits and 70-gene prognosis signature are preserved throughout the metastatic process of breast cancer. Cancer Res 2005, 65:9155-9158.
77. Wilson J.F. The rocky road to useful cancer biomarkers. Ann Intern Med 2006, 144:945-948.
78. Xu L., Tan A.C., Naiman D.Q., Geman D., Winslow R.L. Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinformatics 2005, 21:3905-3911.
79. Yang S., Undar A., Zahn J.D. A microfluidic device for continuous, real time blood plasma separation. Lab Chip 2006, 6:871-880.
80. Zimmermann M., Delamarche E., Wolf M., Hunziker P. Modeling and optimization of high-sensitivity, low-volume microfluidic-based surface immunoassays. Biomed Microdevices 2005, 7:99-110.
81. Contains overviews of systems biology discipline, particularly in "Systems Biology in Depth" section of the website. http://ww.systemsbiology.org.
82. Hood L., Heath J.R., Phelps M.E., Lin B. Systems biology and new technologies enable predictive and preventative medicine. Science 2004, 306:640-643.