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Identifier

000426445

Title

Γονιδιωματική τμηματοποίηση. Διερεύνηση μεθοδολογιών για την τμηματοποίηση ευκαρυωτικών γονιδιωμάτων με συγκεκριμένα χαρακτηριστικά

Alternative Title

Genome Segmentation. Investigation of methodologies for the delination of chromosomal domains with specific characteristics in eukaryotic genomes.

Author

Καλαϊτζάκη, Μαρία Λυδία

Thesis advisor

Νικολάου, Χριστόφορος

Reviewer

Μπερτσιάς, Γεώργιος
Παυλίδης, Παύλος

Abstract

Expanded Next-Generation Sequencing technologies and their improved precision allow for a new approach in the field, which is segmentation of data derived from RNA-Seq experiments, to identify gene clusters, gene boundaries and genes follow a pattern of differential expression. In the present work, the iSeg segmentation method (Girimurugan, SB, et al., 2018), as well as the DFOE method, developed by our team, were used to segment genomes based on gene expression data and identify wider regions. increased expression in one dimension, i.e. in linear chromosomes. RNA-seq analysis was performed on whole blood samples of 200 individuals. 142 individuals were previously diagnosed with TFE and 58 were healthy. The primary conclusion, which came from the application of the DFOE method to the SLE patient data set, was the significantly greater genome coverage of areas of increased expression in patients compared to healthy controls. This coverage was also positively correlated with disease activity, indicating that in addition to elevated expression levels, patients with SLE tend to be over-expressing in targeted regions of the genome. When performing the method of finding statistically significant genomic segments resulting from the DFOE algorithm, we were able to isolate significant regions in both healthy and patients. From further analysis with GprofileR, it was observed that a large proportion of the functions found to be related to the genes of the found fragments are related to TFE disease. The results obtained from the above work appear to be characterized by an abundance of information. Further analysis of the above data could lead to both the identification of disease-related signals and the discovery of new biomarkers.

Language

Greek

Subject

DFOE

ISEG

Lupus

NGS

RNA-SEQ

SLE

Λύκος

Μέθοδοι τμηματοποίησης

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