Computational analysis of heart transcriptome in genetically modified rats
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School of Science |
Master's thesis
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Date
2012
Department
Major/Subject
Informaatiotekniikka
Mcode
T-61
Degree programme
Language
en
Pages
52
Series
Abstract
The transcriptome represents the DNA in the form of mRNA and it encodes proteins. Studying the transcriptome has always given scientists insights into the proteins synthesised in the various regions of the body and its functions. This project deals with the computational analysis of the heart transcriptome of an over-expressing rat and a knockout rat, the outcome of which will shed light on the factors influencing the functioning of the heart. The project was split into three parts. The first two parts dealt with RNASeq analysis of the over-expressing rat where the transcriptome was subjected to differential expression analysis at the gene level and at the exon level respectively. The outcome provided some interesting genes and exons at the top of the list. The gene level analysis was extended to Gene Set Enrichment Analysis and a number of pathways were obtained. The third part of the project dealt with micro array data analysis of knockout rats. The final output showed the obvious differential expression of the knockout gene while the rest of the genes showed minimum variation under normal conditions. Future directions for this project would involve further analysis on the biological aspects of the pathways obtained from the RNASeq data analysis to shed light on the impact of the transgene on them and unravelling other functionalities of the gene while also identifying new and unknown transcripts using tools like Cufflinks and annotating the exons.Description
Supervisor
Lähdesmäki, Harri|Aurell, ErikThesis advisor
Kivelä, RiikkaKeywords
transcriptome, rats, knockout, transgene, RNASeq, microarray, GSEA
