Unit:
Κατεύθυνση Βιοπληροφορική-Υπολογιστική ΒιολογίαLibrary of the School of Science
Supervisors info:
Κωνσταντίνος Βοργίας, Καθηγητής, Τμήμα Βιολογίας, Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών
Original Title:
ΑΝΑΛΥΣΗ ΔΕΔΟΜΕΝΩΝ ΑΠΟ RNA ΑΛΛΗΛΟΥΧΙΣΗ ΜΕ ΧΡΗΣΗ ΣΤΑΤΙΣΤΙΚΩΝ ΜΕΘΟΔΩΝ
Translated title:
STATISTICAL ANALYSIS OF RNA SEQUENCING DATA
Summary:
Skin cutaneous melanoma is considered to be a very aggressive type of cancer and it is definitely one of the most dangerous skin cancers. Therefore, melanoma has two main characteristics that make it a perfect analysis model, there is plenty of information and data available for processing and it is considered to be a contemporary disease. Melanoma was selected as o model disease for differential expression analysis between two different situations. A group of 472 patients / samples was the initial input for the procedures, who were divided into sub-groups based on demographic criteria like age at diagnosis and sex and also, based on genetic criteria, aka the presence or not of a mutated BRAF, RAS family or NF1 genes. A fourth sub-group was also created to include all patients that did not have any of these mutations. The analysis lead to the extraction of lists of differentially expressed genes for each case and comparison. All procedures were implemented using R programming language and more precisely edgeR package. Extracted data were used as an input for BioInfoMiner tool for furthermore analysis, at the level of molecular function. The most interesting analysis was between patients that carry a BRAF mutation and patients without the condition. In this case BioInfoMiner returned results that indicate a relationship between the presence of mutant BRAF gene and the over or under expression of genes that participate in processes like blood vessels generation, inflammatory response and cell adhesion. Further investigation needs to be done.
Main subject category:
Science
Keywords:
RNA, melanoma, skin, differential expression, gene, functional analysis
