Show/Hide Menu
Hide/Show Apps
Logout
Türkçe
Türkçe
Search
Search
Login
Login
OpenMETU
OpenMETU
About
About
Open Science Policy
Open Science Policy
Open Access Guideline
Open Access Guideline
Postgraduate Thesis Guideline
Postgraduate Thesis Guideline
Communities & Collections
Communities & Collections
Help
Help
Frequently Asked Questions
Frequently Asked Questions
Guides
Guides
Thesis submission
Thesis submission
MS without thesis term project submission
MS without thesis term project submission
Publication submission with DOI
Publication submission with DOI
Publication submission
Publication submission
Supporting Information
Supporting Information
General Information
General Information
Copyright, Embargo and License
Copyright, Embargo and License
Contact us
Contact us
Investigating the role of RNA-binding proteins (RBPS) in explaining differential gene expression in cancer
Download
index.pdf
Date
2016
Author
Lafzi, Atefeh
Metadata
Show full item record
Item Usage Stats
291
views
116
downloads
Cite This
Most of the studies on cancer have tried to explain the observed differential gene expression considering only transcriptional regulation. However, post-transcriptional regulation (PTR) has been increasingly recognized as a complex mechanism that also controls various steps of gene expression regulation. Post-transcritional regulation is governed by the interactions of RNA-binding proteins (RBPs) and microRNAs (miRNAs) with their target genes. In this thesis, having found that several RBPs are differentially expressed in Lung squamous cell carcinoma (LUSC), we developed a statistical model which incorporates copy number variation, DNA Methylation and the regulatory effects of transcription factors, miRNAs and RBPs to predict gene expression in cancer. Including RBP-based regulation in addition to other features significantly increased the Spearman rank correlation between predicted and measured expression of held-out genes. Using a feature selection procedure we identified the candidate RBP regulators in LUSC and confirmed that many of them are also differentially expressed. We also determined the targets of these RBPs and compared them with CLIP-determined targets. Lastly, we performed Kaplan-Meier survival analysis, and showed that some of our candidate RBP regulators have prognostic power in LUSC. Our results suggest that the regulatory effects of RBPs have to be considered to explain differential gene expression in cancer.
Subject Keywords
Lungs
,
MicroRNAs.
,
Protein binding.
,
Gene expression.
,
RNA-protein interactions.
URI
http://etd.lib.metu.edu.tr/upload/12619744/index.pdf
https://hdl.handle.net/11511/25451
Collections
Graduate School of Informatics, Thesis
Suggestions
OpenMETU
Core
Evaluation of methylation profiles of an epidermal growth factor receptor gene in a head and neck squamous cell carcinoma patient group
Mutlu, M.; Mutlu, Pelin; Azarkan, S.; Baylr, Ö.; Öcal, B.; Saylam, G.; KORKMAZ, MEHMET HAKAN (2021-03-23)
Upregulation of the epidermal growth factor receptor (EGFR) gene has shown an important impact on the development of head and neck cancers due to its important regulation role on multiple cell signaling pathways. The aim of this study was to investigate the methylation pattern of the promoter region of the EGFR gene between head and neck squamous cell carcinoma (HNSCC) patients and a control group. Forty-seven unrelated HNSCC patients, clinically diagnosed at the Department of Otorhinolaryngology, Dlşkapl Y...
Mathematical Modeling and Approximation of Gene Expression Patterns
Yılmaz, Fatih; Öktem, Hüseyin Avni (2004-09-03)
This study concerns modeling, approximation and inference of gene regulatory dynamics on the basis of gene expression patterns. The dynamical behavior of gene expressions is represented by a system of ordinary differential equations. We introduce a gene-interaction matrix with some nonlinear entries, in particular, quadratic polynomials of the expression levels to keep the system solvable. The model parameters are determined by using optimization. Then, we provide the time-discrete approximation of our time...
Evaluation of Whole Genome Association Study Data in Bipolar Disorders: Potential Novel SNPs and Genes
CENGİZ HAN, Açıkel; Aydın Son, Yeşim; ÇELİK, Cemil; RECEP, Tütüncü (2015-03-01)
Objective: As a result of studies of multifactorial conditions, genetic, physiological and environmental factors, the overall heritability of bipolar disorders has been estimated to be up to 70%. In this study, an analysis of genome-wide association study data using data mining algorithms has revealed single-nucleotide polymorphisms that may be the basis for the molecular etiology of bipolar disorders.
DETERMINATION OF THE RELATIONSHIP BETWEEN DOXORUBICIN RESISTANCE AND WNT SIGNALING PATHWAY IN HELA AND K562 CELL LINES
Mutlu, Pelin; Pourianazar, Negar Taghavi; Yucel, Meral; Gündüz, Ufuk (2018-01-01)
Activation of the Wnt signaling in some types of cancer and its relation with chemotherapy resistance is a very interesting issue that has been emphasized in recent years. Although, it is known that increase in the activity of beta-catenin is important in blast transformation and drug resistance, the underlying mechanisms are still unclear. In this study, changes in the expression levels of 186 genes that are thought to be important in drug resistance and Wnt signaling pathways were determined by using qPCR...
Exploring the relationship between cytoplasmic ion content variation and multidrug resistance in cancer cells via ion-release based impedance spectroscopy
Demircan Yalçın, Yağmur; Sukas, Sertan; Töral, Taylan Berkin; Gündüz, Ufuk; Külah, Haluk (2019-07-01)
This study aimed to measure and compare the cytoplasmic ion concentrations of the parental cells and their drug resistant progenies. High-level laboratory and clinically-relevant multidrug resistance (MDR) cell line models were developed and investigated for K562 and CCRF-CEM cells, respectively. Measurements were achieved using a modified version of ion release-based impedance spectroscopy (IRbIS), where the average total ion concentration per cell was determined by measuring the variations in solution con...
Citation Formats
IEEE
ACM
APA
CHICAGO
MLA
BibTeX
A. Lafzi, “Investigating the role of RNA-binding proteins (RBPS) in explaining differential gene expression in cancer,” M.S. - Master of Science, Middle East Technical University, 2016.