Chapter 2 - University of British Columbia
Chapter 2 - University of British Columbia
Chapter 2 - University of British Columbia
Create successful ePaper yourself
Turn your PDF publications into a flip-book with our unique Google optimized e-Paper software.
<strong>Chapter</strong> 2: SIGMA 2 : A system for the integrative genomic multi-dimensional analysis <strong>of</strong> cancer<br />
genomes, epigenomes, and transcriptomes 1 .............................................................................. 24<br />
2.1 Introduction ........................................................................................................................ 25<br />
2.2 Implementation .................................................................................................................. 26<br />
2.3 Results and discussion ...................................................................................................... 26<br />
2.3.1 Look and feel <strong>of</strong> SIGMA 2 ............................................................................................ 26<br />
2.3.2 Description <strong>of</strong> application scope and functionality ...................................................... 27<br />
2.3.3 Approach to integration between array platforms and assays .................................... 27<br />
2.3.4 Format requirements <strong>of</strong> input data .............................................................................. 27<br />
2.3.5 Description <strong>of</strong> user interface ....................................................................................... 28<br />
2.3.6 Analysis <strong>of</strong> data from a single assay type ................................................................... 29<br />
2.3.7 Analysis <strong>of</strong> data from multiple assays in a given 'omics dimension ............................ 30<br />
2.3.8 Combinatorial analysis <strong>of</strong> multiple 'omics dimensions - gene dosage and gene<br />
expression ........................................................................................................................... 30<br />
2.3.9 Group comparison analysis - single ‘omics dimension ............................................... 31<br />
2.3.10 Group comparison analysis - integrating multiple 'omics dimensions ....................... 31<br />
2.3.11 Multi-dimensional analysis <strong>of</strong> a breast cancer genome ............................................ 31<br />
2.3.12 Exporting data and results ........................................................................................ 32<br />
2.4 Conclusions ....................................................................................................................... 32<br />
2.5 Availability and requirements ............................................................................................ 33<br />
2.6 References ........................................................................................................................ 46<br />
<strong>Chapter</strong> 3: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant<br />
genes and pathways in cancer 2 .................................................................................................. 48<br />
3.1 Background ....................................................................................................................... 49<br />
3.2 Methods ............................................................................................................................. 50<br />
3.2.1 Data generation and acquisition ................................................................................. 50<br />
3.2.2 Data processing and normalization ............................................................................ 51<br />
3.2.3 Strategy for integrative analysis .................................................................................. 52<br />
3.2.4 Multiple concerted disruption (MCD) analysis ............................................................ 53<br />
3.2.5 Simulated data analysis .............................................................................................. 54<br />
3.2.6 Pathway enrichment analysis ..................................................................................... 54<br />
3.2.6 Survival and differential gene expression analysis in publicly available datasets....... 55<br />
3.3 Results and discussion ...................................................................................................... 55<br />
3.3.1 Analysis <strong>of</strong> individual genomic dimensions ................................................................. 55<br />
iv