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DEVELOPMENT AND APPLICATION OF AN I
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Table of Contents Abstract ........
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3.3.2 Multi-dimensional analysis (M
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List of Tables Table 2.1. Features
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Figure 5.3. Overlay of chromosomal
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RB1 Retinoblastoma 1 RNA Ribonuclei
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Dedication To my family. xiii
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Chapter 5: Chari R, Thu KL, Wilson
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1.1 Lung cancer Lung cancer has the
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expression changes are reactive to
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number of different cancer types. M
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large number of tumors, that a give
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(B) By using an integrative approac
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platforms, with one of the latest s
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1.12.1 Development of tools for gen
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quantitative PCR experiments as wel
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1.13 References 1. Jemal A, Siegel
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33. Garber ME, Troyanskaya OG, Schl
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71. Shivapurkar N, Gazdar AF: DNA M
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Chapter 2: SIGMA 2 : A system for t
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Here, we present SIGMA 2 , a novel
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- Page 45 and 46: 2.3.7 Analysis of data from multipl
- Page 47 and 48: expression (Figure 2.8). ERBB2 has
- Page 49 and 50: Figure 2.1 R -Segmentation -Statist
- Page 51 and 52: Figure 2.3 numSamples
- Page 53 and 54: Figure 2.5. Consensus calling and h
- Page 55 and 56: Figure 2.6 HCC2218 HCC2218 HCC2218B
- Page 57 and 58: Figure 2.8. Multi-dimensional persp
- Page 59 and 60: Table 2.1. Features required for in
- Page 61 and 62: 2.6 References 1. Garnis C, Buys TP
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- Page 65 and 66: observed gene expression deregulati
- Page 67 and 68: Raw gene expression profiles from a
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- Page 75 and 76: PTEN expression [44]. Using this pa
- Page 77 and 78: mechanisms at the DNA and RNA level
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- Page 81 and 82: Figure 3.2. Quantitative and qualit
- Page 83 and 84: Figure 3.3 a Proportion of genes in
- Page 85 and 86: 70 Figure 3.5 -log(pvalue) 5.0 4.0
- Page 87 and 88: 72 Figure 3.7 Sample: HCC1008 Copy
- Page 89 and 90: Figure 3.8 a b Proportion of random
- Page 91 and 92: 16. Chari R, Lockwood WW, Coe BP, C
- Page 93: 50. Giovane A, Pintzas A, Maira SM,
- Page 97 and 98: 4.2.3 Determining frequent regions
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- Page 111 and 112: Figure 4.6 a b c Percent of cases A
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- Page 115 and 116: Chr BPStart BPEnd # of Chr BPStart
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- Page 119 and 120: Table 4.5. Cell lines and oncogene
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- Page 123 and 124: 4.6 References 1. Bell DW: Our chan
- Page 125 and 126: 33. Garnis C, Coe BP, Lam SL, MacAu
- Page 127 and 128: 5.1 Introduction In the past decade
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Figure 5.2 # of copies Total copy n
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Figure 5.4. Integration of copy num
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Figure 5.5. Integration of copy num
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Figure 5.6 SHC1 GRB2 SOS2 RRAS ER R
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Figure 5.8 a Log2 Fold Change (T vs
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Figure 5.10 (a) (b) Figure 5.10. Au
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Table 5.2. List of genomic resource
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5.5 References 1. Pinkel D, Segrave
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37. Oliphant A, Barker DL, Stuelpna
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75. Selzer RR, Richmond TA, Pofahl
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111. Melcher R, Al-Taie O, Kudlich
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145. Takai D, Yagi Y, Wakazono K, O
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179. Kondo M, Suzuki H, Ueda R, Osa
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alterations in human prostate cance
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248. Xi L, Feber A, Gupta V, Wu M,
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281. Fernandez-Ranvier GG, Weng J,
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Chapter 6: Conclusions 162
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can identify nearly three times as
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was identified in a small set of sa
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will be done at the pathway level a
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previously described genetic and ep
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16. Zhang K, Li JB, Gao Y, Egli D,
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APPENDIX I: List of publications Th
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This publication is described in se
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This chapter details the technologi
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epigenetic alteration. This led to
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This manuscript describes the curre
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APPENDIX III: Sources of data Sampl
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APPENDIX V: Kaplan-Meier and Oncomi
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APPENDIX VI: Summary of Kaplan-Meie
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