Target Discovery and Validation Reviews and Protocols

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Index 351 conditional by using FRT and LoxP recognition site, 225 Genetic ablation, 181 Genetically altered mouse ES cells, 232 Gene trapping, 183 vectors, 183 Genome engineering, 227 Genome-wide copy number changes, 107 Genome-wide screening, 131 Genomics, 2, 20 Germinal center, 289 Global approaches, 58 Global gene expression, 104 Global techniques, 115 global cDNA technique, 121 β-Globin gene promoter, 173 Gp100, 320 Griseofulvin, 36 H Hammerhead ribozyme, 143 gene-discovery, 143 library, 146 Handling of surgical specimens, 94 Heart failure, 269 murine model, 269 postinfarction congestive heart failure, 271 HeLa S3 cells, 132 Hematopoiesis, 269 Hematopoietic stem cells (HSCs), 279 inhibitors, 273 Hepatitis C, 190 Hierarchical clustering, 95 High-content screening microscopy, 155 High-throughput gene expression, 13 High-throughput screening, 338 HIV-1, 190 Homologous recombination, 170 Homozygous goat lines, 185 HPFT-minigenes, 235 Human endothelium, 264 Human genome U133, 24 Human SIM2, 21 Human tRNAVal promoter, 143 Human umbilical vein-derived endothelial cells (HUVEC), 253 HUVEC/Matrigel assay, 258 Huntington’s disease, 188 I ICOS, 297 Immune tolerance, 279 Immunoediting, 300 Immunoglobulin class-switch recombination, 290 Immunohistochemical markers, 104 Immunological environment, 300 Immunological ignorance, 286 Immunoscreening, 306 Immunosurveillance, 299 Immunotherapy, 319 Innate immunity, 278 Infectious diseases, 189 Infiltrating ductal adenocarcinoma, 57 In silico analysis, 4 Intermediate filament (IF) cytoskeleton, 203 Internal ribosome entry site (IRES), 173 Intrabodies, 176 Invariant chain, 297 K Kaplan-Meier curves, 101 Keratin, 204 assembly, 205 deficient animals, 206 function in cell signaling, 209 function in keratinopathies, 209 gene expression, 208 knockout, 214 modifications, 206 structure, 205 transgenic mice, 214 K5(-/-), 216 K6(-/-), 219 K8(-/-), 214 K10(-/-), 217 K14(-/-), 216 K18(-/-), 215 K19(-/-), 215 Keratin genes, 208 human K18, 208 keratin I gene cluster, 204 keratin II gene cluster, 204 Keratin transgenic, 203 Knockout mice, 6, 203
352 Index L Labeling mRNA, 62 Large-scale gene knockdown, 6 Ligating linkers to cDNA, 71 LipofectAMINE 2000, 148 Listeria monocytogenes, 189 Locus control region (LCR), 173 Luminal epithelial-type tumors, 98 Luminal subtype A group, 101 Luminal subtype B group, 101 M MAGE-1, 320 Male gametes, 169 Mammary tumors, 189 Mass spectrometric analysis of proteins, 61, 65 fractionation, 78 liquid chromatography-tandem mass spectrometry analysis, 80 sample collection and preparation, 77 visualization of proteins, 79 Mass spectrometry, 329 Matrigel, 253 histology and immunohistochemical analysis, 263 Meganucleases, 171 Melan-A, 320 Melanoma antigen-1, 301 Mesothelin, 61 Microarray, 2, 33 Microarray technology, 24, 308 MicroRNAs, 180 Mitomycin C, 98 Molecular profiling, 2 Molecular targets, 61 Myocardial infarction, 13.5 N Naive algorithm, 38 Non-Hodgkin’s B-cell lymphoma, 2 Nonparametric regression model, 47 Notch proteins, 280 O Organogenesis, 184 P Pachyonychia congenita, 207 Pancreatic cancer, 57 Pancreatic juice, 65 Pancreatic tissue, 65 Pancreatitis-associated protein, 62 Pathogen-associated molecular patterns (PAMPs), 278 pcPUR U6i cassette, 133 PCR-based subtraction cloning, 117, 307 Perforin, 299 Peripheral naive T-cells, 293 Peripheral tolerance, 291 Phage display, 302, 336 biopanning, 305 pIII, 303 pVIII, 303 Phenotype-based approach, 6 Plasmid display, 339 Pluripotent cells, 170 Polymerase II promoters, 177 Positive selection, 117 Posttranslational modification, 7 Prion diseases, 187 Profiling cluster, 103 Prognostic factors, 109 Prognostic molecular markers, 109 Programmed death receptor ligand, 297 Promoter methylation, 5 Prostate stem cell antigen (PSCA), 61 Prostate-specific antigen (PSA), 23 Proteasomes, 295 Protein biochips, 339 Protein microarrays, 8, 336 Protein staining, 66 Proteomics, 6, 308, 327, 335 Proximal enhancers, 173 R Random DNA integration, 165 Random integration, 171 Randomized hammerhead ribozymeexpression vector, 145 Receptor editing, 287 Receptor revision, 291 TCR revision, 293 Recombinant proteins, 183
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METHODS IN MOLECULAR BIOLOGY 360 T
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M E T H O D S I N M O L E C U L A R
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© 2007 Humana Press Inc. 999 River
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vi Preface get. Approaches to targe
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viii Contents 10 Transgenic Animal
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x Contributors SAHOHIME MATSUMOTO
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xii Contents of Volume 2 12 Validat
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2 Sioud disease pathogenesis and pe
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4 Sioud A more fruitful approach fo
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6 Sioud both transient and permanen
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8 Sioud serum biomarkers. This syne
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10 Sioud Fig. 2. Schematic of targe
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12 Sioud 13. Magin, T. M. (1998) Le
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Harnessing the Human Genome 15 The
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Harnessing the Human Genome 17 Fig.
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Harnessing the Human Genome 23 The
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Harnessing the Human Genome 27 repr
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Harnessing the Human Genome 29 14.
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Harnessing the Human Genome 31 45.
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34 Imoto et al. (4,5), and Bayesian
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36 Imoto et al. 2. Materials Two ty
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38 Imoto et al. Fig. 3. Graphical v
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40 Imoto et al. Fig. 5. Result of t
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42 Imoto et al. p(D |G) = ∫ p(D,
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44 Imoto et al. β k (k = 1,…,q j
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46 Imoto et al. Fig. 7. Partial res
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48 Imoto et al. Fig. 8. Strategy to
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50 Imoto et al. Fig. 9. (continued)
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52 Imoto et al. Table 3 List of Roo
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54 Imoto et al. 5. De Hoon, M. J. L
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56 Imoto et al. 39. Kamimura, T., S
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58 Beaty et al. cytotoxic drugs and
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60 Beaty et al. Fig. 1. Principles
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62 Beaty et al. oligonucleotide mic
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64 Beaty et al. 3. The 12% polyacry
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66 Beaty et al. 2.3.3. Protein Stai
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68 Beaty et al. 3.1.3. Labeling of
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70 Beaty et al. 1 µL of the anneal
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72 Beaty et al. 4. Phenol:cholorfor
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74 Beaty et al. 19. Wash twice with
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76 Beaty et al. The Following Volum
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78 Beaty et al. using a protein ass
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80 Beaty et al. 6. Shake the gel fo
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82 Beaty et al. Fig. 2. Preparation
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84 Beaty et al. search in. A widely
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86 Beaty et al. 3. Kern, S. E., Hru
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88 Beaty et al. 34. Peters, D. G.,
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5 Molecular Classification of Breas
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Molecular Profiling of Breast Cance
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Fig. 2. (Continued) the right ident
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6 Discovery of Differentially Expre
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Gene Target Discovery 117 In the fi
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Gene Target Discovery 119 sequences
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Gene Target Discovery 121 There is
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Gene Target Discovery 123 digestion
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Gene Target Discovery 125 Fig. 1. P
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Gene Target Discovery 127 5. Sargen
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Gene Target Discovery 129 41. Berry
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132 Matsumoto, Miyagishi, and Taira
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144 Fig. 1. The ribozyme-expression
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146 Sano and Taira 5. 10X L (low-sa
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148 Sano and Taira ribozymes may cl
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150 Fig. 3. A system for the identi
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152 Sano and Taira 4. Notes 1. We r
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9 Production of siRNA- and cDNA-Tra
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Transfected Cell Arrays 157 Fig. 1.
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Transfected Cell Arrays 159 2. The
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Transfected Cell Arrays 161 5. Simp
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164 Houdebine Fig. 1. Different met
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166 Houdebine concentrations become
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168 Houdebine Fig. 2. Major methods
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170 Houdebine integrate into the me
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172 Houdebine 2.2.3. Knock-In Into
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174 Houdebine as insulators. The co
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176 Houdebine Fig. 5. Different met
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178 Houdebine systems. Moreover, st
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180 Houdebine contribute to generat
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182 Houdebine Fig.7. Example of a v
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184 Houdebine more extensively. Tra
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186 Houdebine and stroma. Several o
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188 Houdebine explained at the mole
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190 Houdebine of the intestinal epi
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192 Houdebine interference of the g
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194 Houdebine 17. Whitelaw, C. B. A
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196 Houdebine 51. Bell, A. C., West
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198 Houdebine 86. Carmichael, G. G.
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200 Houdebine 121. Pailhoux, E., Vi
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202 Houdebine 156. Auerbach, A. B.,
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204 Vijayaraj, Söhl, and Magin 1.
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206 Vijayaraj, Söhl, and Magin Fig
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208 Vijayaraj, Söhl, and Magin fil
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210 Table 1 Orthologous Human and M
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212 Table 2 Orthologous Human and M
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214 Vijayaraj, Söhl, and Magin ulc
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216 Vijayaraj, Söhl, and Magin of
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220 Vijayaraj, Söhl, and Magin abs
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222 Vijayaraj, Söhl, and Magin 1.2
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224 Vijayaraj, Söhl, and Magin Fig
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226 Vijayaraj, Söhl, and Magin gen
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230 Vijayaraj, Söhl, and Magin f.
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234 Vijayaraj, Söhl, and Magin b.
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240 Vijayaraj, Söhl, and Magin alt
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242 Table 3 Time Schedule For Aggre
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250 Vijayaraj, Söhl, and Magin 101
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12 The HUVEC/Matrigel Assay An In V
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256 Skovseth, Küchler, and Haralds
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270 Iversen and Sørensen witnessed
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272 Iversen and Sørensen Fig. 1. P
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274 Iversen and Sørensen the core
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14 An Overview of the Immune System
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Overview of Immune System 279 diffe
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Overview of Immune System 281 Fig.
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Overview of Immune System 283 then
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Overview of Immune System 285 expre
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Overview of Immune System 287 Once
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Overview of Immune System 289 solub
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Overview of Immune System 291 amino
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Overview of Immune System 293 (unre
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Overview of Immune System 295 Fig.
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Overview of Immune System 297 the c
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Overview of Immune System 299 (44).
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Page 332 and 333: 15 Potential Target Antigens for Im
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Page 356 and 357: Protein Arrays 343 The ideal proteo
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Page 360 and 361: Protein Arrays 347 49. Yuko Kawahas
Page 362 and 363: Index 349 Index A Acetyl-CoA carbox
Page 366 and 367: Index 353 Recombinant tumor antigen
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