TY  - GEN
UR  - https://archiv.ub.uni-heidelberg.de/volltextserver/12904/
Y1  - 2011///
ID  - heidok12904
TI  - Microarray based transcriptomics and the search for biomarker genes in zebrafish
AV  - public
A1  - Legradi, Jessica
KW  - microarray 
KW  -  zebrafish 
KW  -  biomarker 
KW  -  transcriptionfactor 
KW  -  whole genome
N2  - In the past, zebrafish genes were mapped to human or mouse orthologs in order to perform Gene Ontology or pathway analyses. Therefore, genes without orthologs were removed and zebrafish-specific pathways were not taken into account. After the zebrafish genome has been sequenced almost completely, a growing number of biological databases for zebrafish have been made available. The increasing availability of gene function descriptions and specific pathways improves the applicability of zebrafish for transcriptomics studies. To make full use of the enhanced capabilities, however, new methods need to be developed.  In this thesis, I describe results of two different transcriptional studies. In the first one, I analyzed gene expression data of zebrafish embryos treated with 10 different compounds at 24-48 hpf. I employed multivariate statistical methods to identify compounds that lead to similar expression pattern changes. Furthermore, I tried to identify similarities by comparing co-regulated genes. A gene function analysis of the significantly differentially expressed genes was performed in order to gain a better understanding of the modes of action of the compounds. The findings were validated using literature data. In order to identify biomarker genes, I grouped the compounds based on the identified modes of action and searched for genes that were only de-regulated after treatment with compounds with the same mode of action. I defined sets of biomarker genes for the following modes of action: disruption of mitochondrial potential, Acetylcholinesterase inhibition, Glutathione metabolism, and induction of apoptosis. During the studies of the 10 compounds, it became obvious that commercially available zebrafish microarrays lack several important genes. To overcome this problem, I designed a new array that covers almost the whole zebrafish genome. I could show that the newly designed whole genome array clearly improves microarray experiments.  Additionally, we aimed at gaining deeper insights into the transcriptional regulation during zebrafish development. For this reason, I designed a new microarray consisting only of transcription factors. This array was employed to study six different developmental stages, covering the complete development from egg till larva. We were also interested in variations of transcription factor expression in certain tissues like muscle and brain. The microarray data was analyzed with a newly developed approach using two color arrays to detect expressed transcription factors. Using the new method, I could detect groups of transcription factors that exhibited a similar expression pattern over time. With the help of Gene Ontology, I was able to identify different gene function mechanisms associated with specific developmental stages. Transcription factors with highest expression before gastrulation were mostly involved in protein metabolism, and factors expressed at similar levels during the whole development period were likely to be involved in organ development. Transcription factors with expression peaking at the end of the development seemed to be mostly involved in development of the nervous system and biosynthesis. Additionally, I defined biomarker genes specific for the 6 developmental stages and the tissue samples used in this study.
ER  -