Exploration of methylation-driven mechanisms in cancer

Özer, Buğra (2016) Exploration of methylation-driven mechanisms in cancer. [Thesis]

[thumbnail of Restricted to Repository staff only until 15.04.2019] PDF (Restricted to Repository staff only until 15.04.2019)
Restricted to Repository staff only

Download (2MB) | Request a copy


DNA methylation is an important epigenetic phenomenon that plays a key role in the regulation of expression. For this reason, there have been many studies on the topic of methylation’s role in cancer mechanisms. These studies include analyses based on differential methylation, with the integration of expression information as supporting evidence. In the present study, we firstly focused on defining an optimal analysis strategy when both expression and methylation information are available. We investigated the methylation and expression changes on the genes themselves to have a deeper knowledge of thyroid cancer etiology. Moreover, we explored more important genomic regions considering methylation information and identified common and distinct genes and pathways among different cancer types. In addition, we defined a novel graph-based analysis strategy for identifying methylation-driven potential cancer-causing gene patterns. We applied our method to variety of cancers using the Illumina HumanMethylation450k methylation chip and RNA sequencing data. To extract the significantly altered methylation-driven patterns within a STRING protein-protein interaction network, we first defined a methylation change threshold for “large methylation changes”. Subsequently, in addition to focusing on the interplay between methylation and expression, we carefully considered the individual relationships between different genes to ensure a deeper understanding of the methylome and transcriptome. Furthermore, we studied the presence of shared and distinct features among the different types of cancers using hierarchical clustering analysis. Overall, our work not only defined a novel approach for the identification of significantly altered methylation-driven pathways but it also contributed to improving our knowledge of the etiologies of different cancers and the common and distinct features among them.
Item Type: Thesis
Additional Information: Yükseköğretim Kurulu Tez Merkezi Tez No: 434056.
Uncontrolled Keywords: Transcriptomics. -- Epigenetics. -- Data analysis. -- Data integration. -- Cancer Biology. -- Protein-protein interaction network. -- Functional enrichment analysis. -- Transkriptomiks. -- Data analizi. -- Data entegrasyonu. -- Kanser. -- Kanser biyolojisi. -- Protein-protein etkileşim ağı. -- Fonksiyonel zenginleştirme analizi.
Subjects: T Technology > TA Engineering (General). Civil engineering (General) > TA164 Bioengineering
Divisions: Faculty of Engineering and Natural Sciences > Academic programs > Biological Sciences & Bio Eng.
Faculty of Engineering and Natural Sciences
Depositing User: IC-Cataloging
Date Deposited: 14 May 2018 11:49
Last Modified: 26 Apr 2022 10:24
URI: https://research.sabanciuniv.edu/id/eprint/34825

Actions (login required)

View Item
View Item