Target Discovery and Validation Reviews and Protocols

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Contributors ROBERT M. BEATY • Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD LINA CEKAITE • Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, University of Oslo, Oslo, Norway HOLGER ERFLE • Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany MADS GRONBORG • McKusick–Nathans Institute of Genetic Medicine; Departments of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark GUTTORM HARALDSEN • Institute of Pathology, Rikshospitalet University Hospital, Oslo, Norway LOUIS-MARIE HOUDEBINE • Biologie du Developpement et Reproduction, Institut National de la Recherche Agronomique, Paris, France EIVIND HOVIG • Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, University of Oslo, Oslo, Norway SEIYA IMOTO • Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan PER OLE IVERSEN • Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway DIRK JÄGER • Medizinische Onkologie, Nationales Centrum für Tumorerkrankungen, Universitätsklinikum Heidelberg, Heidelberg, Germany AXEL M. KÜCHLER • Institute of Pathology, Rikshospitalet University Hospital, Oslo, Norway FRANÇOIS LE NAOUR • INSERM V602, Hôpital Paul Brousse, Villejuif, France THOMAS M. MAGIN • Institut für Physiologische Chemie, Abteilung für Zellbiochemie, Bonner Forum Biomedizin and LIMES, Universitätsklinikum Bonn, Bonn, Germany ANIRBAN MAITRA • Departments of Pathology and Oncology, The Sol Goldman Pancreatic Cancer Research Center and McKusick–Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD ix
x Contributors SAHOHIME MATSUMOTO • Department of Chemistry and Biotechnology, School of Engineering, Tokyo, Japan MAKOTO MIYAGISHI • Gene Function Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan SATORU MIYANO • Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan RAMASWAMY NARAYANAN • Center for Molecular Biology and Biotechnology and Department of Biology, Florida Atlantic University, Boca Raton, FL RAINER PEPPERKOK • Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany JONATHAN R. POLLACK • Departments of Pathology and Oncology, The Sol Goldman Pancreatic Cancer Research Center and McKusick–Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD ØYSTEIN RØSOK • Department of Immunology, Institute for Cancer Research, The Norwegian Radium Hospital, University of Oslo, Oslo, Norway MASAYUKI SANO • Gene Function Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan CHRISTOPHER J. SAVOIE • Gene Networks International, Tokyo, Japan MOULDY SIOUD • Department of Immunology, Institute for Cancer Research, The Norwegian Radium Hospital, University of Oslo, Oslo, Norway DAG K. SKOVSETH • Institute of Pathology, Rikshospitalet University Hospital, Oslo, Norway GORAN SÖHL • Institut für Physiologische Chemie, Abteilung für Zellbiochemie, Bonner Forum Biomedizin and LIMES, Universitätsklinikum Bonn, Bonn, Germany DAG R. SØRENSEN • Centre of Comparative Medicine, Rikshospitalet University Hospital, Oslo, Norway THERESE SØRLIE • Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, University of Oslo, Oslo, Norway KAZUNARI TAIRA • Department of Chemistry and Biotechnology, School of Engineering, Tokyo, Japan YOSHINORI TAMADA • Institute of Statistical Mathematics, Tokyo, Japan PREETHI VIJAYARAJ • Institut für Physiologische Chemie, Abteilung für Zellbiochemie, Bonner Forum Biomedizin and LIMES, Universitätsklinikum Bonn, Bonn, Germany
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
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Page 13 and 14: xii Contents of Volume 2 12 Validat
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Page 17 and 18: 4 Sioud A more fruitful approach fo
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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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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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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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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 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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