Target Discovery and Validation Reviews and Protocols

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Index 349 Index A Acetyl-CoA carboxylase 2 (ACAC2), 6 Adaptive immunity, 278 Adjuvant therapy, 103 Aggregation, 241 tetraploid-diploid embryos, 241 Allelic exclusion, 287 Alloantibodies, 300 Alloantigens, 300 Alzheimer’s disease, 186 Anergy, 287 Angiogenesis, 253 dependent diseases, 254 inhibitors, 257 Antibody microarray, 338 Antifungal drug, griseofulvin, 50 Antigen processing, 294 Class I pathway, 294 Class II pathway, 295 Antigen-presenting cells (APCs), 279 Antisense, 23 Antisense fingerprint of genes, 26 Apoptosis, 132 Atherosclerosis, 188 Autoantibodies, 331, 338 Autoantigen array, 338 Autoimmune disease, 9, 338 Autoimmunity, 294 Autologous typing, 300 B BAGE, 320 Basal stratified epithelia, 216 Bayesian networks, 34, 40, 47 Bayes statistics, 41 B-cell, 278 affinity maturation, 288 anergy, 287 antigen receptor, 281 B1 cells, 289 349 B2 cells, 289 development and maturation, 287 follicular cells, 289 marginal zone, 289 naive cells, 289 negative selection, 287 plasma and memory, 298 pre-B-cell antigen receptor (BCR), 286 receptor editing, 287 transmembrane proteins Igα and Igβ, 287 Biochemical approach, 301 Bioinformatics, 3, 77 approaches, 13 Blastocyst injections, 237 Boolean network, 37 BRCA1 gene, 104 mutations, 104 Breast cancer, 2, 322 Breast tumors, 91 clinical implications, 101 molecular classification, 91 molecular portraits, 104 prediction, 103 prognosis, 101 C Cancer diseases, 91 Cancer Gene Anatomy Project (CGAP), 13 Cancer gene discovery, 13 Cancer genomics, 109 Cancer vaccines, 310 dendritic cells, 310 CCR5 receptor, 190 CD28 family, 297 CD31, 257 cDNA expression library, 321, 339 cDNA libraries, 302 Cell arrays, 155 transfected with siRNAs or cDNAs, 155 Central tolerance, 285
350 Index Centroblast, 289 Centrocytes, 289 Centrosome/microtubule-associated coiledcoil protein (CSPP), 2 Cellular system, 34 Chimeric mice, Claudin 4, 61 c-myc, 189 Common lymphoid progenitor (CLP), 280 production, 237 Conditional alleles, 226 Conditional transgene expression, 181 Conventional prognostic factors, 102 Colorectal cancer, 18 Cre-lox system, 9 Cre-loxP, 172 Cytokines, 270 Cytotoxic T-lymphocyte, 320 Creutzfeldt-Jakob disease, 25, 187 Cyclin D1, 189 Cystic fibrosis, 186 D 1D gel electrophoresis, 65 Degenerative diseases, 187 Dendritic cells, 292 Differential display (DD), 120 Differential screening, 116 Differentially expressed genes, 115 Digital analysis of gene expression, 15 Digital differential display (DDD), 16 Disease-causing mutations, 203 DNA methylation, 179 DNA microarrays, 7, 58, 67, 93, 124 hybridization, 68 microarray imaging, 68 preparation of mRNA, 67 DNA microinjection, 165 in cytoplasm, 166 DNA transfer by using electroporation, 166 Down syndrome, 21 DP thymocytes, 286 Drug-active pathway, 34, 47 Drug-affected genes, 34 Drug discovery, 9 Druggable genes, 34, 46 Drug target discovery, 33 Drug target validation, 33 E Early endosome, 297 Ectodermal dysplasia, 218 Embryonic stem (ES) cells, 227 double replacement, 235 electroporation, 234 feeder cells, 233 freezing of cells, 236 isolation of DNA for PCR-based genotyping, 235 karyotyping, 236 thawing and plating cells, 233 Embryos, two- and eight-cell recovery, 239 Endostatin, 258 Endothelial cells, 254 transfer into RAG2 knockout mice, 263 Epidermolysis bullosa simplex, 207 Epidermolytic hyperkeratosis, 207 Episomal vectors, 169 Epitope spreading, 310 ERBB2+ amplification, 103 ERBB2+ subtypes, 101 Expressed sequence tag (EST) sequences, 121 Expression profiling, 307 F Fas-mediated cytotoxicity, 299 Filamentous M13 bacteriophages, 336 First- and second-strand cDNA synthesis, 64, 70 Flp-FRT systems, 172 5-Fluorouracil, 98 Follicular dendritic cells, 290 Forward genetics, 5 Functional analysis, 159, 203 G Gene cluster, 99 Gene expression patterns, 94 Gene knockdown, 176 Gene knockout, 170, 176 Gene network, 4, 33 Gene profiling, 4 Gene-targeting, 224 double replacement procedure, 225 conditional by using three LoxP recognition sites, 225
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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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78 Beaty et al. using a protein ass
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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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184 Houdebine more extensively. Tra
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186 Houdebine and stroma. Several o
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204 Vijayaraj, Söhl, and Magin 1.
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12 The HUVEC/Matrigel Assay An In V
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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 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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Page 366 and 367: Index 353 Recombinant tumor antigen
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