Target Discovery and Validation Reviews and Protocols

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Harnessing the Human Genome 31 45. DeYoung, M. P., Tress, M., and Narayanan, R. (2003) Down’s syndrome-associated Single Minded 2 gene as a pancreatic cancer drug therapy target. Cancer Lett. 200, 25–31. 46. Goolsby, M. J. (2001) Use of PSA measurement in practice. J. Am. Acad. Nurse Pract. 13, 246–248. 47. Aleman, M. J., DeYoung, M. P., Tress, M., Keating, P., Perry, G. W., and Narayanan, R. (2005) Inhibition of single minded 2 gene expression mediates tumor-selective apoptosis and differentiation in human colon cancer cells. Proc. Natl. Acad. Sci. USA 102, 12,765–12,770. 48. Ratan, R. R. (2003) Mining genome databases for therapeutic gold: SIM2 is a novel target for treatment of solid tumors. Trends Pharmacol. Sci. 24, 508–510. 49. Touchette, N. (2003) Mouse-to-mouse revelation: genome yields cancer drug target. Genome News Network. http://www.genomenewsnetwork.org/articles/ 04_03.mouse.shtml. April 18, 2003. 50. Nambu, J. R., Lewis, J. O., Wharton, K. A., Jr., and Crews, S. T. (1991) The Drosophila single-minded gene encodes a helix-loop-helix protein that acts as a master regulator of CNS midline development. Cell 67, 1157–1167. 51. Benbow, L., Wang, L., Laverty, M., et al. (2002) A reference database for tumorrelated genes co-expressed with interleukin-8 using genome-scale in silico analysis. BMC Genomics 3, 29.
Page 1 and 2: METHODS IN MOLECULAR BIOLOGY 360 T
Page 3 and 4: M E T H O D S I N M O L E C U L A R
Page 5 and 6: © 2007 Humana Press Inc. 999 River
Page 7 and 8: vi Preface get. Approaches to targe
Page 9 and 10: viii Contents 10 Transgenic Animal
Page 11 and 12: x Contributors SAHOHIME MATSUMOTO
Page 13 and 14: xii Contents of Volume 2 12 Validat
Page 15 and 16: 2 Sioud disease pathogenesis and pe
Page 17 and 18: 4 Sioud A more fruitful approach fo
Page 19 and 20: 6 Sioud both transient and permanen
Page 21 and 22: 8 Sioud serum biomarkers. This syne
Page 23 and 24: 10 Sioud Fig. 2. Schematic of targe
Page 25 and 26: 12 Sioud 13. Magin, T. M. (1998) Le
Page 28 and 29: Harnessing the Human Genome 15 The
Page 30 and 31: Harnessing the Human Genome 17 Fig.
Page 36 and 37: Harnessing the Human Genome 23 The
Page 40 and 41: Harnessing the Human Genome 27 repr
Page 42 and 43: Harnessing the Human Genome 29 14.
Page 46 and 47: 3 Analysis of Gene Networks for Dru
Page 48 and 49: Gene Networks 35 Fig. 1. Conceptual
Page 50 and 51: Gene Networks 37 Table 1 List of 12
Page 52 and 53: Gene Networks 39 Fig. 4. Downstream
Page 54 and 55: Gene Networks 41 Fig. 6. Directed a
Page 56 and 57: Gene Networks 43 where Γ ( . ) is
Page 58 and 59: Gene Networks 45 r is the dimension
Page 60 and 61: Gene Networks 47 Table 2 Druggable
Page 62 and 63: Gene Networks 49 network and nonpar
Page 64 and 65: Gene Networks 51 Fig. 9. (A) Identi
Page 66 and 67: Gene Networks 53 Bayesian network w
Page 68 and 69: Gene Networks 55 23. Tinerey, L. an
Page 70 and 71: 4 Target Discovery and Validation i
Page 72 and 73: Pancreatic Cancer 59 on the microar
Page 74 and 75: Pancreatic Cancer 61 1.4. Mass Spec
Page 76 and 77: Pancreatic Cancer 63 3. Yeast tRNA
Page 78 and 79: Pancreatic Cancer 65 2.2.10. Purifi
Page 80 and 81: Pancreatic Cancer 67 3. Methods 3.1
Page 82 and 83: Pancreatic Cancer 69 3.1.5. Washing
Page 84 and 85: Pancreatic Cancer 71 3.2.4. Ligatin
Page 86 and 87: Pancreatic Cancer 73 3.2.9. Isolati
Page 88 and 89: Pancreatic Cancer 75 14. Vortex the
Page 90 and 91: Pancreatic Cancer 77 11. Incubate o
Page 92 and 93: Pancreatic Cancer 79 Approximately
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Pancreatic Cancer 81 in many ways.
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Pancreatic Cancer 83 3.3.10. Sample
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Pancreatic Cancer 85 can be achieve
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Pancreatic Cancer 87 19. Argani, P.
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Pancreatic Cancer 89 49. Rabilloud,
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92 Sørlie
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94 Sørlie are based on such a plat
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Fig. 2. Cluster analysis of a subse
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98 Sørlie are not internally heter
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100 Sørlie termed luminal subtype
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102 Sørlie Fig. 4. Kaplan-Meier an
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104 Sørlie this cluster of genes v
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106 Sørlie Fig. 5. Cluster of gene
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108 Sørlie Fig. 6. Concordance bet
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110 Sørlie Acknowledgments All col
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112 Sørlie 31. Slamon, D. J., Clar
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114 Sørlie 62. Bergh, J., Norberg,
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116 Røsok and Sioud 1.1. Selection
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118 Røsok and Sioud Compared with
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120 Røsok and Sioud 1.1.7. Differe
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122 Røsok and Sioud a powerful app
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124 Røsok and Sioud represent each
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126 Røsok and Sioud splicing may b
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128 Røsok and Sioud 22. Liang, P.
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7 Genome-Wide Screening by Using Sm
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RNAi Libraries 133 Fig. 2. Schemati
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RNAi Libraries 135 pathways. Thus,
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RNAi Libraries 137 3.3.1. Puromysin
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RNAi Libraries 139 Fig. 4. Example
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RNAi Libraries 141 12. Paddison, P.
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8 Hammerhead Ribozyme-Based Target
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Hammerhead Ribozymes 145 Libraries
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Hammerhead Ribozymes 147 3.1.1. Pre
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149 Fig. 2. Discovery of genes invo
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Hammerhead Ribozymes 151 3.3. Recov
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Hammerhead Ribozymes 153 9. Onuki,
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156 Erfle and Pepperkok 2. Material
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158 Erfle and Pepperkok cells away
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160 Erfle and Pepperkok 5. The stai
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10 Transgenic Animal Models in Biom
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Transgenic Models 165 giant mice ex
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Transgenic Models 167 2.1.3. Use of
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Transgenic Models 169 a recombinant
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Transgenic Models 171 Fig. 3. Diffe
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Transgenic Models 173 FRT sites are
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Transgenic Models 175 Fig. 4. Diffe
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Transgenic Models 177 models, the b
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Transgenic Models 179 Fig. 6. Vecto
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Transgenic Models 181 vectors can d
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Transgenic Models 183 then used to
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Transgenic Models 185 be fixed and
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Transgenic Models 187 period of inc
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Transgenic Models 189 (142). Genes
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Transgenic Models 191 from differen
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Transgenic Models 193 Acknowledgmen
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Transgenic Models 195 34. Thermes,
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Transgenic Models 197 68. Gupta, S.
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Transgenic Models 199 105. Weber, W
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Transgenic Models 201 138. Ranger,
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11 Keratin Transgenic and Knockout
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Keratin Transgenics and Knockouts 2
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211 K17 K17 Hair follicles, Alopeci
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213 K6a K6a Hair follicles; Lysis o
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254 Skovseth, Küchler, and Haralds
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In Vivo Assay of Human Angiogenesis
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13 A Murine Model for Studying Hema
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Heart Failure and Immunity 271 We h
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Heart Failure and Immunity 273 3.1.
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Heart Failure and Immunity 275 6. W
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278 Sioud gene products have been d
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280 Sioud Fig. 1. Schematic of hema
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282
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284
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286 Sioud selection), whereas thymo
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288 Sioud Fig. 5. Affinity maturati
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290 Sioud Fig. 6. A second signal i
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292 Sioud Fig. 7. Bridging between
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294 Sioud Fig. 8. Schematic of clas
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296 Sioud Fig. 10. Critical molecul
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298 Sioud In contrast to the expres
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300 Sioud tumor infiltrating lympho
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302 Sioud (see Chapter 15, Volume 1
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304 Sioud display if the foreign pr
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306 Sioud Fig. 13. Immunoscreening
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308 Sioud molecular techniques have
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310 Sioud Although much of the init
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312 Sioud Because of their importan
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314 Sioud 22. He, X., Janeway, C. A
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316 Sioud 59. Sahin, U., Tureci, O.
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318 Sioud 91. Golgher, D., Jones, E
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320 Jäger Furthermore, this immune
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322 Jäger Antigens that are tumor-
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324 Jäger 2. Nakano, O., Sato, M.,
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326 Jäger 31. Chen, Y. T., Gure, A
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328 Le Naour dependent on CD8+ cyto
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330 Le Naour Fig. 1. To illustrate
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332 Le Naour heterogeneity of HCC,
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334 Le Naour 15. Le Naour, F., Mise
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336 Cekaite, Hovig, and Sioud Yeast
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338 Cekaite, Hovig, and Sioud diffe
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340
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342 Cekaite, Hovig, and Sioud nonra
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344 Cekaite, Hovig, and Sioud 3. Ue
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346 Cekaite, Hovig, and Sioud 32. T
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348 Cekaite, Hovig, and Sioud 65. L
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350 Index Centroblast, 289 Centrocy
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352 Index L Labeling mRNA, 62 Large
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354 Index Tetraploid embryos, 239 g
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