Dna methylation thesis

Assessing the relationship between DNA methylation and gene expression in germ cell tumours

Enter your search terms. Genetic variation and DNA methylation in the context of neurological disease.

Downloads since deposit. Download activity - last month. Download activity - last 12 months. This observation confirmed that DNA methylation profiles can distinguish the invasive group from the non-invasive group of melanoma cell lines. The RNA-Seq results identified interesting genes which were associated with growth factor binding, transmembrane receptor kinase activity, cell adhesion and extra cellular matrix organization.

Of these 17 genes, AVPI1 was selected for further validation because it had significant promoter hypermethylation in the invasive cell lines compared to non-invasive cell lines.

  1. Using DNA methylation to study benign breast and breast tumours.
  2. Using DNA methylation to study benign breast and breast tumours.
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  6. TET-dependent DNA methylation patterns in mammalian development and disease.
  7. Associated Data.

In addition, low expression of this gene was identified in the invasive cell lines, and this was associated with MAPK activity and epithelial sodium channel ENaC downregulation. Functional analysis suggested that AVPI1 promoter methylation may be associated indirectly with melanoma invasion through an intermediate mechanism of ENaC regulation and epithelial mesenchymal transition EMT.

Overall, this study has provided novel insights into distinct DNA methylation profiles between invasive and non-invasive melanoma cell lines, which predominantly included cell lines derived from New Zealand metastatic melanoma patients. Integrative analysis of DNA methylation and gene expression revealed potential genes involved in the invasive phenotype of melanoma, which was followed by functional analysis of AVPI1 to investigate its role in the invasive phenotype. These investigations of AVPI1 and other genes identified from the integrative analysis of DNA methylation and gene expression have provided a platform, which can further be used to establish their role in phenotype switching.

Interaction of omega-3 fatty acids and cytokine gene DNA methylation

Advisor: Eccles, Michael R. Degree Name: Doctor of Philosophy. Degree Discipline: Department of Pathology. Publisher: University of Otago. Research Type: Thesis. Existing methods are limited in terms of detection sensitivity as well as time and memory consumption.

UC San Diego

Our approach is based on a circular binary segmentation, using a scoring function to detect sub-regions that show a stronger difference between the mean methylation levels of two groups than the surrounding background. These sub-regions are tested using a two-dimensional Kolmogorov Smirnov test 2D-KS test [Fasano ] for significant differences taking all samples of each group into account.

The use of the non-parametric 2D-KS test allows to avoid assumptions about a background distribution. Furthermore, the two dimensions of the problem, i.

Associated Data

The algorithm calls DMRs in sufficiently short time on single sample comparisons as well as on about 50 samples per group. Furthermore, it works on whole-genome bisulfite sequencing WGBS and reduced representation bisulfite sequencing RRBS data and is able so estimate missing data points from the methylation rates of other samples in the group.

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  • Benchmarks on simulated and real data sets show that metilene outperforms other existing methods and is especially suitable for noisy datasets often found for example in cancer analysis. In the framework of this thesis, the previously introduced methods and algorithms are used to analyze a WGBS dataset of two different subtypes of germinal-center derived B-cell lymphomas and healthy controls. In both lymphoma subgroups genome-wide hypomethylation was found, with an exception for a specific type of promoter regions, i.

    What is epigenetics? - Carlos Guerrero-Bosagna

    Using the previously presented algorithm, DMRs were called between the three entities. A strong enrichment of DMRs immediately downstream of the transcription start site was observed, indicating the regulatory relevance of this regions.