Differential gene expression analysis of RNA-Seq data: Comparing lung squamous cell carcinoma and healthy lung cells in Homo sapiens

Κώτσα, Χριστίνα; Kotsa, Christina

dc.contributor.author	Κώτσα, Χριστίνα	el
dc.contributor.author	Kotsa, Christina	en
dc.date.accessioned	2025-01-08T11:57:46Z
dc.date.available	2025-01-08T11:57:46Z
dc.identifier.uri	https://dspace.lib.ntua.gr/xmlui/handle/123456789/60656
dc.identifier.uri	http://dx.doi.org/10.26240/heal.ntua.28352
dc.description	Εθνικο Μετσόβιο Πολυτεχνείο--Μεταπτυχιακή Εργασία.Διεπιστημονικό-Διατμηματικό Πρόγραμμα Μεταπτυχιακών Σπουδων(Δ.Π.Μ.Σ) "Μεταφραστική Βιοιατρική Μηχανικής και Επιστήμης"	el
dc.rights	Αναφορά Δημιουργού - Παρόμοια Διανομή 3.0 Ελλάδα	*
dc.rights	Αναφορά Δημιουργού - Παρόμοια Διανομή 3.0 Ελλάδα	*
dc.rights.uri	http://creativecommons.org/licenses/by-sa/3.0/gr/	*
dc.subject	Differential gene expression analysis	en
dc.subject	RNA-Seq	en
dc.subject	Αλληλούχιση RNA	el
dc.subject	Ανάλυση διαφορικής γονιδιακής έκφρασης	el
dc.subject	Lung cancer	en
dc.subject	Καρκίνος του πνεύμονα	el
dc.subject	Next generation sequencing	en
dc.subject	Αλληλούχιση επόμενης γενιάς	el
dc.subject	Bioinformatics	en
dc.subject	Βιοπληροφορική	el
dc.title	Differential gene expression analysis of RNA-Seq data: Comparing lung squamous cell carcinoma and healthy lung cells in Homo sapiens	en
dc.title	Ανάλυση διαφορικής γονιδιακής έκφρασης δεδομένων RNA-Seq: Σύγκριση καρκινώματος πλακωδών κυττάρων πνεύμονα και υγιών πνευμονικών κυττάρων στον άνθρωπο	el
heal.type	masterThesis
heal.classification	Bioinformatics	en
heal.classification	Βιοπληροφορική	el
heal.language	en
heal.access	campus
heal.recordProvider	ntua	el
heal.publicationDate	2024-06-20
heal.abstract	Differential gene expression (DGE) analysis of RNA sequencing (RNA-seq) data has become a powerful tool in understanding the molecular mechanisms underlying various diseases. This thesis presents an in-depth examination of RNA-seq methodologies and their applications in the context of human disease, focusing on the DE analysis of RNA-Seq data derived from human lung squamous cell carcinoma and normal lung tissues. The thesis begins with a brief but comprehensive introduction to the biology of RNA, describing the different types of RNAs and their functions in cellular processes. This is followed by a discussion of the basic concepts of human disease, particularly cancer, and how they relate to genetic and epigenetic factors, laying the foundation for understanding the importance of RNA analysis in disease research. Subsequently, the revolutionary technology of Next-Generation Sequencing (NGS) is presented, focusing on RNA-Seq. All the critical steps of an RNA-seq experimental procedure are discussed, including RNA extraction, quality control, mRNA enrichment, fragmentation, library preparation, and sequencing. The introductory part of the thesis then focuses on explaining in detail the analysis of the acquired RNA-Seq data; which is the procedure we followed in this thesis. In this RNA-seq analysis project, the initial steps involved selecting and downloading the dataset of interest from an online database. This process was followed by quality control checks to ensure the reliability of the dataset for the subsequent analyses. Based on the quality control, the data were then trimmed to improve the overall quality, which was checked again. The trimmed reads were then aligned to the human genome in order to gain insights into the level of gene expression in cancer and normal cells. After counting aligned reads, the next essential step is to normalize them.This process accounts for factors that prevent direct comparison of expression reads, thereby making the data biologically meaningful. The normalized data underwent differential expression analysis to identify the up- and down- regulated genes in cancer cells. The results of the differentially expressed genes were then plotted using various graphs, revealing a variety of information about our dataset. The final step of this project was the enrichment analysis, which revealed significantly enriched molecular functions, biological processes, and pathways in this type of non-small cell lung cancer. Our analysis revealed important differences in gene expression in tumor and normal cells. Through enrichment analysis we were able to identify several enriched functions and pathways commonly found in cancer according to the literature. Our findings contribute to a better understanding of squamous cell lung carcinoma and highlight potential biomarkers and therapeutic targets for this disease.	en
heal.advisorName	Matsopoulos, George	en
heal.committeeMemberName	Matsopoulos, George	en
heal.committeeMemberName	Panagopoulos, Athanasios	en
heal.committeeMemberName	Tsanakas, Panayiotis	en
heal.academicPublisher	Εθνικό Μετσόβιο Πολυτεχνείο. Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών	el
heal.academicPublisherID	ntua
heal.numberOfPages	84 σ.	el
heal.fullTextAvailability	false