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Epigenetic modelling: DNA methylation and working towards model parameterisation

Porwal, Jyoti (2011) Epigenetic modelling: DNA methylation and working towards model parameterisation. Master of Science thesis, Dublin City University.

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Abstract

The main focus of the research in this thesis is the investigation in DNA methylation mechanisms of epigenetics and the study of a specific database. As part of the latter work, the role of curation is described, and a new knowledge management system, PathEpigen1 , is reported that is currently being developed for colon cancer in the Sci-Sym centre. The database deals with genetic and epigenetic interactions and contains considerable data on molecular events such as genetic and epigenetic events. The data curation includes biomedical and biological information. An efficient method was devised to extract biological information from the literature to process, manage and upgrade data. We present a Deterministic Finite Automata (DFA) model for the DNA methylation mechanism controlled by DNA methyltransferase (DNMT) enzymes. This thesis provides a brief introduction to epigenetics, a survey of ongoing research on computational epigenetics and a description of the DNA methylation database. Furthermore, it also gives an overview of DNA methylation and its importance in cancer. The DFA models three states of methylation frequency (normal, de-novo and hypermethylated) in the cell. It has been executed on input of random strings of size 100. Out of the strings considered, we found that 26%, 37% and 37% correspond to normal, de-novo (cancer initiation) and hypermethylated (cancer) states, respectively.

Item Type:Thesis (Master of Science)
Date of Award:November 2011
Refereed:No
Supervisor(s):Ruskin, Heather J.
Uncontrolled Keywords:epigenetic signature; DNA methyltransferase; hypermethylation; CpG islands; micromodel basis
Subjects:Biological Sciences > Bioinformatics
Computer Science > Computational complexity
DCU Faculties and Centres:DCU Faculties and Schools > Faculty of Engineering and Computing > School of Computing
Use License:This item is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 3.0 License. View License
Funders:SFI
ID Code:16505
Deposited On:02 Dec 2011 14:07 by Heather Ruskin. Last Modified 02 Dec 2011 14:07

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