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Differential Gene expression using a negative binomial model
Janáková, Tereza ; Tkacz, Ewaryst (oponent) ; Abo Khayal, Layal (vedoucí práce)
The main goal of this master thesis is to carry out the analysis of differential gene expression using a negative binomial model. The first part is devoted to theoretical basis, discusses the RNA sequencing, Next-Generation Sequencing (NGS), the benefits and applications, and FASTAQ format. The second part is the practical part, there was chosen a suitable data set of genes, that will be later analyzed, and the relevant data was downloaded. This data was aligned to the human genome version 37 by Burrows-Wheeler transform and the SAM formatted files were created using the Bowtie mapper. The SAM formatted files were sorted by SAMtools. In the following part of this work was created an annotation object of target genes using Ensembl´s BioMart service and Matlab (version R2013b). Next, digital gene expression was determined and library size factor was estimated. In the end the negative binomial distribution parameters were estimated and data was tested for a differential gene expression.
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