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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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.
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