Chapter 2 - University of British Columbia

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Page 1 and 2: DEVELOPMENT AND APPLICATION OF AN I
Page 3 and 4: Table of Contents Abstract ........
Page 5 and 6: 3.3.2 Multi-dimensional analysis (M
Page 7 and 8: List of Tables Table 2.1. Features
Page 9 and 10: Figure 5.3. Overlay of chromosomal
Page 11 and 12: RB1 Retinoblastoma 1 RNA Ribonuclei
Page 13 and 14: Dedication To my family. xiii
Page 15 and 16: Chapter 5: Chari R, Thu KL, Wilson
Page 17 and 18: 1.1 Lung cancer Lung cancer has the
Page 19 and 20: expression changes are reactive to
Page 21 and 22: number of different cancer types. M
Page 23 and 24: large number of tumors, that a give
Page 25 and 26: (B) By using an integrative approac
Page 27 and 28: platforms, with one of the latest s
Page 29 and 30: 1.12.1 Development of tools for gen
Page 31 and 32: quantitative PCR experiments as wel
Page 33: 1.13 References 1. Jemal A, Siegel
Page 37 and 38: 71. Shivapurkar N, Gazdar AF: DNA M
Page 39 and 40: Chapter 2: SIGMA 2 : A system for t
Page 41 and 42: Here, we present SIGMA 2 , a novel
Page 43 and 44: datasets. To utilize this, the user
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
Page 63 and 64: Chapter 3: An integrative multi-dim
Page 65 and 66: observed gene expression deregulati
Page 67 and 68: Raw gene expression profiles from a
Page 69 and 70: screening approach to gene amplific
Page 71 and 72: many regions of frequent LOH/AI do
Page 73 and 74: approach to examining the whole gen
Page 75 and 76: PTEN expression [44]. Using this pa
Page 77 and 78: mechanisms at the DNA and RNA level
Page 79 and 80: In this study, three DNA dimensions
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 and 94:
50. Giovane A, Pintzas A, Maira SM,
Page 95 and 96:
4.1 Introduction Genetic alteration
Page 97 and 98:
4.2.3 Determining frequent regions
Page 99 and 100:
etween loss and UPD (Figure 4.3). S
Page 101 and 102:
obtained, profiled and used as the
Page 103 and 104:
Figure 4.1. Detection of UPD using
Page 105 and 106:
Figure 4.2. Comparison of frequent
Page 107 and 108:
Figure 4.3 Gain Loss 642 441 7 Figu
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94 Figure 4.4 1 2 3 4 5 6 7 8 9 10
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Figure 4.6 a b c Percent of cases A
Page 113 and 114:
Figure 4.7 a b 6p25.3 Log2 fold cha
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Chr BPStart BPEnd # of Chr BPStart
Page 117 and 118:
Table 4.3. Overlap of oncogenes in
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Table 4.5. Cell lines and oncogene
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Table 4.7. RefSeq genes in focal re
Page 123 and 124:
4.6 References 1. Bell DW: Our chan
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33. Garnis C, Coe BP, Lam SL, MacAu
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5.1 Introduction In the past decade
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polymorphism (SNP) arrays with over
Page 131 and 132:
substitutions) and UV exposure (C t
Page 133 and 134:
developed antibodies and methylated
Page 135 and 136:
Histone modification states. While
Page 137 and 138:
metastasis [226]. High throughput a
Page 139 and 140:
Implications on sample size require
Page 141 and 142:
analyzed using the "minet" package
Page 143 and 144:
expression. The next challenge is t
Page 145 and 146:
Figure 5.2 # of copies Total copy n
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Figure 5.4. Integration of copy num
Page 149 and 150:
Figure 5.5. Integration of copy num
Page 151 and 152:
Figure 5.6 SHC1 GRB2 SOS2 RRAS ER R
Page 153 and 154:
Figure 5.8 a Log2 Fold Change (T vs
Page 155 and 156:
Figure 5.10 (a) (b) Figure 5.10. Au
Page 157 and 158:
Table 5.2. List of genomic resource
Page 159 and 160:
5.5 References 1. Pinkel D, Segrave
Page 161 and 162:
37. Oliphant A, Barker DL, Stuelpna
Page 163 and 164:
75. Selzer RR, Richmond TA, Pofahl
Page 165 and 166:
111. Melcher R, Al-Taie O, Kudlich
Page 167 and 168:
145. Takai D, Yagi Y, Wakazono K, O
Page 169 and 170:
179. Kondo M, Suzuki H, Ueda R, Osa
Page 171 and 172:
alterations in human prostate cance
Page 173 and 174:
248. Xi L, Feber A, Gupta V, Wu M,
Page 175 and 176:
281. Fernandez-Ranvier GG, Weng J,
Page 177 and 178:
Chapter 6: Conclusions 162
Page 179 and 180:
can identify nearly three times as
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was identified in a small set of sa
Page 183 and 184:
will be done at the pathway level a
Page 185 and 186:
previously described genetic and ep
Page 187 and 188:
16. Zhang K, Li JB, Gao Y, Egli D,
Page 189 and 190:
APPENDIX I: List of publications Th
Page 191 and 192:
This publication is described in se
Page 193 and 194:
This chapter details the technologi
Page 195 and 196:
epigenetic alteration. This led to
Page 197 and 198:
This manuscript describes the curre
Page 199 and 200:
APPENDIX III: Sources of data Sampl
Page 201 and 202:
APPENDIX V: Kaplan-Meier and Oncomi
Page 203 and 204:
APPENDIX VI: Summary of Kaplan-Meie
Page 205:
University of British Columbia - Br
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