Target Discovery and Validation Reviews and Protocols

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Gene Target Discovery 127 5. Sargent, T. D. and Dawid, I. B. (1983) Differential gene expression in the gastrula of Xenopus laevis. Science 222, 135–139. 6. Timberlake, W. E. (1980) Developmental gene regulation in Aspergillus nidulans. Dev. Biol. 78, 497–510. 7. Hedrick, S. M., Cohen, D. I., Nielsen, E. A., and Davis, M. M. (1984) Isolation of cDNA clones encoding T cell-specific membrane-associated proteins. Nature 308, 149–153. 8. Sagerstrom, C. G., Sun, B. I., and Sive, H. L. (1997) Subtractive cloning: past, present, and future. Annu. Rev. Biochem. 66, 751–783. 9. Rubenstein, J. L., Brice, A. E., Ciaranello, R. D., Denney, D., Porteus, M. H., and Usdin, T. B. (1990) Subtractive hybridization system using single-stranded phagemids with directional inserts. Nucleic Acids Res. 18, 4833–4842. 10. Rothstein, J. L., Johnson, D., Jessee, J., et al. (1993) Construction of primary and subtracted cDNA libraries from early embryos. Methods Enzymol. 225, 587–610. 11. Houge, G. (1993) Simplified construction of a subtracted cDNA library using asymmetric PCR. PCR Methods Appl. 2, 204–209. 12. Wang, Z. and Brown, D. D. (1991) A gene expression screen. Proc. Natl. Acad. Sci. USA 88, 11,505–11,509. 13. Yokota, H. and Oishi, M. (1990) Differential cloning of genomic DNA: cloning of DNA with an altered primary structure by in-gel competitive reassociation. Proc. Natl. Acad. Sci. USA 87, 6398–63402. 14. Hubank, M. and Schatz, D. G. (1999) cDNA representational difference analysis: a sensitive and flexible method for identification of differentially expressed genes. Methods Enzymol. 303, 325–349. 15. Lisitsyn, N., Lisitsyn, N., and Wigler, M. (1993) Cloning the differences between two complex genomes. Science 259, 946–951. 16. Hubank, M. and Schatz, D. G. (1994) Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucleic Acids Res. 22, 5640–5648. 17. Diatchenko, L., Lau, Y. F., Campbell, A. P., et al. (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93, 6025–6030. 18. Siebert, P. D., Chenchik, A., Kellogg, D. E., Lukyanov, K. A., and Lukyanov, S. A. (1995) An improved PCR method for walking in uncloned genomic DANN. Nucleic Acids Res. 23, 1087, 1088. 19. Gurskaya, N. G., Diatchenko, L., Chenchik, A., et al. (1996) Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. Anal. Biochem. 240, 90–97. 20. Lukyanov, K., Diatchenko, L., Chenchik, A., et al. (1997) Construction of cDNA libraries from small amounts of total RNA using the suppression PCR effect. Biochem. Biophys. Res. Commun. 230, 285–288. 21. Leirdal, M., Shadidy, M., Rosok, O., and Sioud, M. (2004) Identification of genes differentially expressed in breast cancer cell line SKBR3: potential identification of new prognostic biomarcers. Int. J. Mol. Med. 14, 217–222.
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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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Page 104 and 105: 5 Molecular Classification of Breas
Page 106 and 107: Molecular Profiling of Breast Cance
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Page 130 and 131: Gene Target Discovery 117 In the fi
Page 132 and 133: Gene Target Discovery 119 sequences
Page 134 and 135: Gene Target Discovery 121 There is
Page 136 and 137: Gene Target Discovery 123 digestion
Page 138 and 139: Gene Target Discovery 125 Fig. 1. P
Page 142: Gene Target Discovery 129 41. Berry
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Page 159 and 160: 146 Sano and Taira 5. 10X L (low-sa
Page 161 and 162: 148 Sano and Taira ribozymes may cl
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Page 165 and 166: 152 Sano and Taira 4. Notes 1. We r
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Page 177 and 178: 164 Houdebine Fig. 1. Different met
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Page 187 and 188: 174 Houdebine as insulators. The co
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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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218 Vijayaraj, Söhl, and Magin sug
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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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228 Vijayaraj, Söhl, and Magin the
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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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