Target Discovery and Validation Reviews and Protocols

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Contents Preface .................................................................................................. v Contributors ......................................................................................... ix Contents of Volume 2 .......................................................................... xi 1 Main Approaches to Target Discovery and Validation Mouldy Sioud .............................................................................. 1 2 Bioinformatics Approaches to Cancer Gene Discovery Ramaswamy Narayanan ........................................................... 13 3 Analysis of Gene Networks for Drug Target Discovery and Validation Seiya Imoto, Yoshinori Tamada, Christopher J. Savoie, and Satoru Miyano................................................................ 33 4 Target Discovery and Validation in Pancreatic Cancer Robert M. Beaty, Mads Gronborg, Jonathan R. Pollack, and Anirban Maitra............................................................... 57 5 Molecular Classification of Breast Tumors: Toward Improved Diagnostics and Treatments Therese Sørlie ........................................................................... 91 6 Discovery of Differentially Expressed Genes: Technical Considerations Øystein Røsok and Mouldy Sioud .......................................... 115 7 Genome-Wide Screening by Using Small-Interfering RNA-Expression Libraries Sahohime Matsumoto, Makoto Miyagishi, and Kazunari Taira.............................................................. 131 8 Hammerhead Ribozyme-Based Target Discovery Masayuki Sano and Kazunari Taira ........................................ 143 9 Production of siRNA and cDNA-Transfected Cell Arrays on Noncoated Chambered Coverglass for High-Content Screening Microscopy in Living Cells Holger Erfle and Rainer Pepperkok ........................................ 155 vii
viii Contents 10 Transgenic Animal Models in Biomedical Research Louis-Marie Houdebine .......................................................... 163 11 Keratin Transgenic and Knockout Mice: Functional Analysis and Validation of Disease-Causing Mutations Preethi Vijayaraj, Goran Söhl, and Thomas M. Magin .......... 203 12 The HUVEC/Matrigel Assay: An In Vivo Assay of Human Angiogenesis Suitable for Drug Validation Dag K. Skovseth, Axel M. Küchler, and Guttorm Haraldsen . 253 13 A Murine Model for Studying Hematopoiesis and Immunity in Heart Failure Per Ole Iversen and Dag R. Sørensen .................................... 269 14 An Overview of the Immune System and Technical Advances in Tumor Antigen Discovery and Validation Mouldy Sioud .......................................................................... 277 15 Potential Target Antigens for Immunotherapy Identified by Serological Expression Cloning (SEREX) Dirk Jäger ................................................................................ 319 16 Identification of Tumor Antigens by Using Proteomics François Le Naour................................................................... 327 17 Protein Arrays: A Versatile Toolbox for Target Identification and Monitoring of Patient Immune Responses Lina Cekaite, Eivind Hovig, and Mouldy Sioud..................... 335 Index ................................................................................................. 349
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: vi Preface get. Approaches to targe
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
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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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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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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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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 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 297 the c
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Overview of Immune System 299 (44).
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Overview of Immune System 301 demon
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Overview of Immune System 307 some
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Overview of Immune System 309 sera
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Overview of Immune System 313 measu
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Overview of Immune System 315 42. H
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Overview of Immune System 317 74. D
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15 Potential Target Antigens for Im
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Tumor Antigen Discovery 321 develop
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Tumor Antigen Discovery 323 panel b
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Tumor Antigen Discovery 325 16. Joc
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16 Identification of Tumor Antigens
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Immunoproteomics 329 by “shot gun
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Immunoproteomics 331 isoelectric fo
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Immunoproteomics 333 3. 2D-PAGE is
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17 Protein Arrays A Versatile Toolb
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Protein Arrays 337 Table 1 Classifi
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Protein Arrays 339 fractions from c
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Protein Arrays 341 combinatorial sc
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Protein Arrays 343 The ideal proteo
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Protein Arrays 345 18. Cekaite, H.
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Protein Arrays 347 49. Yuko Kawahas
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Index 349 Index A Acetyl-CoA carbox
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Index 351 conditional by using FRT
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Index 353 Recombinant tumor antigen
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