Transcriptomics: Translation of Global Expression Analysis to Genomic Medicine

Genomic and Personalized Medicine, Two-Vol Set

Volumn , Issue , 2009, Pages 143-156

  Kittleson, Michelle M ^a   Irizarry, Rafael ^b   Heidecker, Bettina ^c   Hare, Joshua M ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^c UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84884796632     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-369420-1.00012-3     Document Type: Chapter

References (59)

1. Albelda S.M., Sheppard D. Functional genomics and expression profiling: Be there or be square. Am J Respir Cell Mol Biol 2000, 23:265-269.
2. Alizadeh A., Eisen M., Davis R.E., Ma C., Sabet H., Tran T., Powell J.I., Yang L., Marti G.E., Moore D.T., et al. The lymphochip: A specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harb Symp Quant Biol 1999, 64:71-78.
3. Barrans J.D., Stamatiou D., Liew C.C. Construction of a human cardiovascular cDNA microarray: Portrait of the failing heart. Biochem Biophys Res Comm 2001, 280:964-969.
4. Birney E., Stamatoyannopoulos J.A., Dutta A., Guigo R., Gingeras T.R., Margulies E.H., Weng Z.P., Snyder M., Dermitzakis E.T., Stamatoyannopoulos J.A., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
5. Bolstad B.M., Collin F., Simpson K.M., Irizarry R.A., Speed T.P. Experimental design and low-level analysis of microarray data. Int Rev Neurobiol 2004, 60:25-58.
6. Bolstad B.M., Irizarry R.A., Gautier L., Wu Z. Preprocessing High-density Oligonucleotide Arrays. Bioinformatics and Computational Biology Solutions Using R and Bioconductor 2005, 13-32. Springer, New York. R. Gentleman, V.J. Carey, W. Huber, R.A. Irizarry, S. Dudoit (Eds.).
7. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29:365-371.
8. Bullinger L., Dohner K., Bair E., Frohling S., Schlenk R.F., Tibshirani R., Dohner H., Pollack J.R. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med 2004, 350:1605-1616.
9. Butte A. The use and analysis of microarray data. Nat Rev Drug Discov 2002, 1:951-960.
10. Calin G.A., Ferracin M., Cimmino A., Di Leva G., Shimizu M., Wojcik S.E., Iorio M.V., Visone R., Sever N.I., Fabbri M., et al. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 2005, 353:1793-1801.
11. Chen H.Y., Yu S.L., Chen C.H., Chang G.C., Chen C.Y., Yuan A., Cheng C.L., Wang C.H., Terng H.J., Kao S.F., et al. A five-gene signature and clinical outcome in non-small-cell lung cancer. N Engl J Med 2007, 356:11-20.
12. Cook S.A., Rosenzweig A. DNA microarrays: Implications for cardiovascular medicine. Circ Res 2002, 91:559-564.
13. Cui X., Hwang J.T., Qiu J., Blades N.J., Churchill G.A. Improved statistical tests for differential gene expression by shrinking variance components estimates. Biostatistics 2005, 6:59-75.
14. Deng M.C., Eisen H.J., Mehra M.R., Billingham M., Marboe C.C., Berry G., Kobashigawa J., Johnson F.L., Starling R.C., Murali S., et al. Noninvasive discrimination of rejection in cardiac allograft recipients using gene expression profiling. Am J Transplant 2006, 6:150-160.
15. Depre C., Shipley G.L., Chen W., Han Q., Doenst T., Moore M.L., Stepkowski S., Davies P.J., Taegtmeyer H. Unloaded heart in vivo replicates fetal gene expression of cardiac hypertrophy. Nat Med 1998, 4:1269-1275.
16. DePrimo S.E., Wong L.M., Khatry D.B., Nicholas S.L., Manning W.C., Smolich B.D., O'Farrell A.M., Cherrington J.M. Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: A novel strategy for biomarker identification. BMC Cancer 2003, 3:3.
17. 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.
18. Dudoit S., Fridlyand J., Speed T.P. Comparison of discrimination methods for the classification of tumors using gene expression data. J. Am. Stat Assoc 2002, 97:77-87.
19. Dudoit S., Schaffer J.P., Boldrick J.C. Multiple hypothesis testing in microarray experiments. Stat Sci 2003, 18:71-103.
20. Eshaque B., Dixon B. Technology platforms for molecular diagnosis of cystic fibrosis. Biotechnol Adv 2006, 24:86-93.
21. 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.
22. Hall J.L., Grindle S., Han X., Fermin D., Park S., Chen Y., Bache R.J., Mariash A., Guan Z., Ormaza S. Genomic profiling of the human heart before and after mechanical support with a ventricular assist device reveals alterations in vascular signaling networks. Physiol Genomics 2004, 17:283-291.
23. Heidecker B., Hare J.M. The use of transcriptomic biomarkers for personalized medicine. Heart Fail Rev 2007, 12:1-11.
24. Horwitz P.A., Tsai E.J., Putt M.E., Gilmore J.M., Lepore J.J., Parmacek M.S., Kao A.C., Desai S.S., Goldberg L.R., Brozena S.C., et al. Detection of cardiac allograft rejection and response to immunosuppressive therapy with peripheral blood gene expression. Circulation 2004, 110:3815-3821.
25. Ishii M., Hashimoto S., Tsutsumi S., Wada Y., Matsushima K., Kodama T., Aburatani H. Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis. Genomics 2000, 68:136-143.
26. Jackson R.J., Standart N. How do microRNAs regulate gene expression? Sci STKE 2007, re1.
27. Jongeneel C.V., Iseli C., Stevenson B.J., Riggins G.J., Lal A., Mackay A., Harris R.A., O'Hare M.J., Neville A.M., Simpson A.J., et al. Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci U S A 2003, 100:4702-4705.
28. Kendziorski C., Irizarry R.A., Chen K.S., Haag J.D., Gould M.N. On the utility of pooling biological samples in microarray experiments. Proc Natl Acad Sci U S A 2005, 102:4252-4257.
29. Kendziorski C.M., Newton M.A., Lan H., Gould M.N. On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Stat Med 2003, 22:3899-3914.
30. Kim J.B., Porreca G.J., Song L., Greenway S.C., Gorham J.M., Church G.M., Seidman C.E., Seidman J.G. Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 2007, 316:1481-1484.
31. Kittleson M.M., Hare J.M. Molecular signature analysis: The potential of gene expression analysis in cardiomyopathy. Future Cardiol 2005.
32. Kittleson M.M., Ye S.Q., Irizarry R.A., Minhas K.M., Edness G., Conte J.V., Parmigiani G., Miller L.W., Chen Y., Hall J.L., et al. Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation 2004, 110:3444-3451.
33. Lapointe J., Li C., Higgins J.P., van de R.M., Bair E., Montgomery K., Ferrari M., Egevad L., Rayford W., Bergerheim U., et al. Gene expression profiling identifies clinically relevant subtypes of prostate cancer. Proc Natl Acad Sci U S A 2004, 101:811-816.
34. Lash A.E., Tolstoshev C.M., Wagner L., Schuler G.D., Strausberg R.L., Riggins G.J., Altschul S.F. SAGEmap: A public gene expression resource. Genome Res 2000, 10:1051-1060.
35. Liew C.C. Expressed genome molecular signatures of heart failure. Clin Chem Lab Med 2005, 43:462-469.
36. Liu E.T., Karuturi K.R. Microarrays and clinical investigations. N Engl J Med 2004, 350:1595-1597.
37. Lonnstedt I., Speed T.P. Replicated microarray data. Statistical Sinica 2002, 12:31-46.
38. Lossos I.S., Czerwinski D.K., Alizadeh A.A., Wechser M.A., Tibshirani R., Botstein D., Levy R. Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes{AQ10}. N Engl J Med 2004, 350:1828-1837.
39. Ma J., Liew C.C. Gene profiling identifies secreted protein transcripts from peripheral blood cells in coronary artery disease. J Mol Cell Cardiol 2003, 35:993-998.
40. Margulies K.B., Matiwala S., Cornejo C., Olsen H., Craven W.A., Bednarik D. Mixed messages. Transcription patterns in failing and recovering human myocardium. Circ Res 2005, 1-8.
41. Morello F., de Bruin T.W., Rotter J.I., Pratt R.E., van der Kallen C.J., Hladik G.A., Dzau V.J., Liew C.C., Chen Y.D. Differential gene expression of blood-derived cell lines in familial combined hyperlipidemia. Arterioscler Thromb Vasc Biol 2004, 24:2149-2154.
42. Pomeroy S.L., Tamayo P., Gaasenbeek M., Sturla L.M., Angelo M., McLaughlin M.E., Kim J.Y., Goumnerova L.C., Black P.M., Lau C., et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 2002, 415:436-442.
43. Prober J.M., Trainor G.L., Dam R.J., Hobbs F.W., Robertson C.W., Zagursky R.J., Cocuzza A.J., Jensen M.A., Baumeister K. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 1987, 238:336-341.
44. Ritchie, M.E., Diyagama, D., Neilson, van Laar, R., Dobrovic, A., Holloway, A. and Smyth, G.K. (2006). Empirical array quality weights for microarray data. Submitted{AQ11}.
45. Rogers Y.H., Venter J.C. Genomics: Massively parallel sequencing. Nature 2005, 437:326-327.
46. Rosenwald A., Wright G., Chan W.C., Connors J.M., Campo E., Fisher R.I., Gascoyne R.D., Muller-Hermelink H.K., Smeland E.B., Giltnane J.M., et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 2002, 346:1937-1947.
47. Salvado C.S., Trounson A.O., Cram D.S. Towards preimplantation diagnosis of cystic fibrosis using microarrays. Reprod Biomed Online 2004, 8:107-114.
48. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977, 74:5463-5467.
49. Seo D., Wang T., Dressman H., Herderick E.E., Iversen E.S., Dong C., Vata K., Milano C.A., Rigat F., Pittman J., et al. Gene expression phenotypes of atherosclerosis. Arterioscler Thromb Vasc Biol 2004, 24:1922-1927.
50. Simon R., Radmacher M.D., Dobbin K., McShane L.M. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003, 95:14-18.
51. Smyth G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:1-27.
52. Storey J.D. A direct approach to false discovery rates. J Roy Stat Soc B 2002, 479-498.
53. Tan P.K., Downey T.J., Spitznagel E.L., Xu P., Fu D., Dimitrov D.S., Lempicki R.A., Raaka B.M., Cam M.C. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 2003, 31:5676-5684.
54. Tibshirani R., Hastie T., Narasimhan B., Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A 2002, 99:6567-6572.
55. Tusher V.G., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98:5116-5121.
56. Twine N.C., Stover J.A., Marshall B., Dukart G., Hidalgo M., Stadler W., Logan T., Dutcher J., Hudes G., Dorner A.J., et al. Disease-associated expression profiles in peripheral blood mononuclear cells from patients with advanced renal cell carcinoma. Cancer Res 2003, 63:6069-6075.
57. Valk P.J., Verhaak R.G., Beijen M.A., Erpelinck C.A., Barjesteh van Waalwijk van Doorn-Khosrovani, Boer J.M., Beverloo H.B., Moorhouse M.J., van der Spek P.J., Lowenberg B., Delwel R. Prognostically useful gene-expression profiles in acute myeloid leukemia. N Engl J Med 2004, 350:1617-1628.
58. 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.
59. van R.E., Sutherland L.B., Qi X., Richardson J.A., Hill J., Olson E.N. Control of stress-dependent cardiac growth and gene expression by a microRNA. Science 2007, 316:575-579.