Master Thesis Defense: Ece Egemen
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Ece Egemen
Computer Science and Engineering, MSc Thesis, 2013 

Thesis Jury
Prof. Dr. Uğur Osman Sezerman (Thesis Supervisor), Assoc. Prof. Berrin Yanıkoğlu, Assoc. Prof. Yücel Saygın, Assoc. Prof. Devrim Gözüaçık, Asst. Prof. Kemal Kılıç

Date &Time: August,13th, 2013 – 13:00

Place: FENS L056

Keywords: Epigenetics, CpG Island Methylation, Epilepsy-related Pathways.


Epilepsy is a disorder which affects approximately 1% of the world’s population. It is possible to explain the underlying mechanisms of epilepsy by not only alterations in genetic structure and environmental factors, but also epigenetic mechanisms. As a significant epigenetic modification, DNA methylation may play a crucial role for understanding biological pathways related to epilepsy.

Even though the relationship between CpG islands, DNA methylation and gene expression is quite complex, in this thesis we aimed to determine significant biological pathways related to epilepsy, using the difference of methylation levels at CpG loci in family trios. Dataset was gathered from 10 family trios (30 individuals total) and it includes methylation level information for each CpG locus determined by Illumina HumanMethylation450 Bead Chip which is a microarray based analysis tool. Considering the difference of methylation levels at each CpG locus, we prepared lists of genes that we marked as significant. Applying several filters to the dataset allowed us to gather more reliable information from the dataset. We identified a number of significant pathways that may be related to epilepsy.