1. Introduction
2. Chapter 1: 2D-DIGE
   1. Journal of Proteome Research; IF:5.684
      1. Intro
         1. Neoplastic Transformation
         2. Breast Cancer Metastasis
         3. Previous Work by Tollefsbol
         4. 2D-DIGE
      2. Methods
      3. Results
         1. Transformation Data
         2. Representative Gel and design
         3. Spots and Peaks
         4. Expression Graphs
         5. Maspin Data
      4. Discussion
3. Chapter 2: HNF4a in Breast Metastasis
   1. Journal: Molecular Cancer; IF: 5.36
      1. Intro
         1. Neoplastic Transformation
         2. Gene ST Array
         3. Ingenuity Pathway Analysis
         4. Bone and Brain Metastasis
         5. Proteomics Paper
      2. Methods
         1. Filters
         2. IPA methods
      3. Results
         1. Functional Analysis
            1. THMEC
         2. Network Analysis
            1. Brain
            2. THMEC
      4. Discussion
4. Chapter 3: In silico based method
   1. Journal: Bioinformatics; IF: 4.328
      1. Intro
         1. Epigenetics
         2. Epigenetic Modulators
         3. DMRs
         4. Bivalent Domains
         5. HNF4a paper
      2. Methods
      3. Results
         1. Epigenetic Modulators
            1. THMEC
            2. Site Mets
         2. DMRs
            1. THMEC
            2. Site Mets
         3. Bivalent Domains
            1. THMEC
            2. Site Mets
      4. Discussion
5. Chapter 4: Theory on the origin of Cancer
   1. Journal of Theoretical Biology; IF 2.54
      1. Intro
      2. Body
      3. Discussion
6. Chpater 5:Hypermethylation in Oncogenesis
7. Chapter 6: MIRA Methods Chapter
   1. Epigenetic Protocols Book
8. General Discussion