Time series analysis of gene expression regulation profiles in early mouse development

Kozić, Zrinko (2013) Time series analysis of gene expression regulation profiles in early mouse development. Diploma thesis, Faculty of Science > Department of Biology.

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Abstract

Mammalian preimplantation development is a period starting with the fertilization of the oocyte and ending with the implantation of blastocyst into the wall of the uterus. This is a period where dynamic changes in gene expression are regulated through various mechanisms, which act on both transcriptional and non-transcriptional levels. High-throughput research of genetic regulation during development is done in form of time-course expression analysis. RNA-seq is a method of sequencing the total cellular mRNA and provides a capability of unbiased transcriptome analysis and expression quantification. Mouse cells in early developmental stages were analysed using RNA-seq in order to quantify the expression through the time-course. I identified differentially expressed genes and clustered them into expression profiles using unsupervised machine learning methods. I searched the profiles for enrichment of functional elements and sequence motifs recognized by DNA binding transcription factors. Results show that genes can be clustered by their expression patterns into distinct groups, thus enabling the observation of significant changes in expression. Functional elements related to gene expression were assigned to profiles. Finally, I identified the transcription factors that may influence the regulation of expression.

Item Type: Thesis (Diploma thesis)
Keywords: RNA-seq, expression profiling, k-means, functional annotation, motif enrichment, transcription factors
Supervisor: Vlahoviček, Kristian
Date: 2013
Number of Pages: 36
Subjects: NATURAL SCIENCES > Biology
Divisions: Faculty of Science > Department of Biology
Depositing User: Silvana Šehić
Date Deposited: 30 Sep 2014 09:29
Last Modified: 30 Sep 2014 09:29
URI: http://digre.pmf.unizg.hr/id/eprint/2876

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