DNA microarrays [Elektronische Ressource] : applications and novel approaches for analysis and interpretation / vorgelegt von Julia Cathérine Engelmann

Sujets

• Biologie

Informations

• Publié par: julius-maximilians-universitat_wurzburg
• Publié le: 01 janvier 2008
• Nombre de lectures: 13
• Langue: English
• Poids de l'ouvrage: 9 Mo

Extrait

DNA microarrays: applications and novel approaches for
analysis and interpretation.
Dissertation zur Erlangung des
naturwissenschaftlichen Doktorgrades
der Bayerischen Julius-Maximilians-Universit¨at Wurzburg¨
vorgelegt von
Julia Cath´erine Engelmann
aus Wetzlar
Wurzburg¨ , 2008Eingereicht am:.............................................................
Mitglieder der Promotionskommission:
Vorsitzender: Prof. Dr. Martin J. Mulle¨ r
Gutachter: Prof. Dr. Thomas Dandekarhter: Prof. Dr. Sven Rahmann
Tag des Promotionskolloquiums:............................................
Doktorurkunde ausgeh¨andigt am:...........................................Acknowledgments
IwouldliketoexpressmygratitudetomyacademicadvisorsProf. Thomas
Dandekar and Dr. Tobias Muller¨ for their guidance and constant support in
helping me to conduct and complete this work. In addition, I want to thank
Prof. Sven Rahmann for serving on my advisory committee, as well as for
his excellent advice. I am thankful to IZKF B-36 and BMBF project FUN-
CRYPTA (FKZ 0313838B) for funding. Thanks to my collaborators who have
contributed experimental work, advice, fruitful discussions and provided lab
facilities to complete the projects described in this thesis. I am also grateful to
Molecular Ecology Resources journalforthepermissiontoprintmypublication
“Modeling cross-hybridization on phylogenetic DNA microarrays increases the
detection power of closely related species” in this thesis.
Many thanks to all the people I have come to know in the Department of
Bioinformatics at the University of Wurzburg¨ , whose friendship I always en-
joyed. Specialthankstothebestroommatesintown,TorbenFriedrich,Philipp
Seibel, Juilee Thakar and Stefan Pinkert. Thanks to Karin Schleinkofer, Kor-
nelia Neveling and Frank F¨orster for proof-reading parts of this thesis. A big
thank you goes to Kornelia Neveling for always being there when I needed a
friend.
I owe everything to my family who has supported and encouraged me over
the years. I especially want to thank Sven for his inspiration and continuous
encouragementduringmystudies. Finally,Iwanttoexpressmydeepestappre-
ciation to my beloved parents for their love, affection, and unlimited support
during my life and studies.Contents
I General Introduction 1
II Results 15
1 Modeling cross-hybridization on phylogenetic DNA microar-
rays increases the detection power of closely related species 17
2 Unsupervisedmeta-analysisondiversegeneexpressiondatasets
allows insight into gene function and regulation 39
3 Is gene activity in plant cells affected by UMTS irradiation?
A whole genome approach. 63
4 An integrated view of gene expression and solute profiles of
Arabidopsis tumors: A genome-wide approach 97
5 Genome Expression Pathway Analysis Tool - Analysis and vi-
sualizationofmicroarraygeneexpressiondataundergenomic,
proteomic and metabolic context 117
6 Explorative data analysis of MCL reveals gene expression net-
works implicated in survival and prognosis supported by ex-
plorative CGH analysis 131
7 Germinal Center B cell-like (GCB) and Activated B cell-like
(ABC) type of diffuse large B cell lymphoma: Analysis of
molecular predictors, signatures, cell cycle state and patient
survival 165
III Concluding Discussion 189
Summary 199
Zusammenfassung 201
Bibliography 205
vvi CONTENTS
Contributions 212
Curriculum Vitae 215
List of Publications 216Part I
General Introduction
13
Thesis Outline
In this thesis, applications of the microarray technology to answer biological
questions as well as novel approaches for microarray data analysis are pre-
sented. Among others, microarrays can be used to provide a snapshot of the
transcriptionlevelofthousandsofgenessimultaneously,whichisamaintheme
of this thesis.
Part I gives an introduction into the microarray technology and analysis.
In the individual chapters of part II, the main part of this thesis, the results of
theexperimentsandanalysesconductedduringmyPhDstudiesarepresented.
The first publication presented in Part II is concerned with the question how
biodiversity studies interrogating the species composition of a certain habi-
tat could be improved using the microarray technology. Existing microarray
approaches are typically based on the evaluation of unprocessed signal inten-
sities of the individual species spots. For very closely related species, however,
cross-hybridizationimpedesspeciesdetectionbasedonsignalintensitiesalone.
IpresentinthisthesisthedesignofaphylogeneticDNAmicroarrayandanovel
approach for its data analysis. Using simple linear regression modeling on the
signal intensities, I could show that this analysis approach greatly improves
the resolution of phylogenetic DNA microarrays for species detection.
The second publication, chapter 2 of part II, addresses the question of
how the large amounts of gene expression microarray datasets which have
accumulatedinpublic repositories can effectively be integrated into a coherent
analysis. While several studies have integrated microarray data targeting the
same biological question, approaches to integrate data from a wide range of
experimental conditions are missing. In chapter 2, I present an explorative
meta-analysis approach exemplified on Arabidopsis thaliana datasets which
makes use of the large amounts of microarray gene expression data stored in
public databases.
In later chapters of part II, I describe projects using microarrays for gene
expression profiling to answer a defined biological question. One experiment
was conducted to find out if microwave irradiation has an effect on the tran-
scription levels of an Arabidopsis thaliana cell culture (publication/chapter 3).
With explorative analysis methods, I found that the irradiation had an ef-
fect on gene expression, but this effect was very small and might not have an
influence on the physiology of a whole plant.
To answer the question how plant tumors differ from normal inflorescence
tissue and how they sustain growth, another gene expression microarray ex-
periment was performed and is described here. Microarray data and solute
measurements were used to characterize Arabidopsis thaliana tumors by their
transcription and solute profiles (publication/chapter 4). Among others, the
results showed that the plant tumor cells change from an auxotrophic to a
heterotrophic metabolism. The tumor acts like a sink tissue, reducing its pho-
tosynthesis to a minimum and accumulating nutrients from the host plant.
Besides using the microarray technology to answer biological questions, I
alsoparticipatedinthedevelopmentofanewapproachtointegratemicroarray4 I. GENERAL INTRODUCTION
gene expression data with other data types (publication/chapter 5). Integra-
tion of gene expression with chromosomal localization, functional annotation
or other high-throughput data can facilitate the interpretation of microarray
experiment results. The web application and database GEPAT allows inte-
grating microarray data results with other data types like annotation data on
gene function, protein interactions or CGH data. GEPAT has been used to
analyze a data set of Mantle Cell Lymphoma (MCL) patients consisting of
gene expression microarray and CGH (Comparative Genomic Hybridization)
data which is described in publication/chapter 6. The last chapter of the re-
sults part presents a re-analysis of Diffuse Large B-cell Lymphoma (DLBCL)
gene expression data revealing regulation differences between long and short
surviving patients.
The results of part II are discussed in a concluding discussion in part III.
The microarray technology
Thecentralpartandcommonthemeofthisthesisistheanalysisofmicroarray
data. Except the first publication which describes the development and analy-
sisofaphylogeneticDNAmicroarray, theindividualpublicationsofthisthesis
areconcernedwithmeasuringandanalyzinggeneexpressionlevelstoanswera
biologicalquestion. Thereasontostudygeneexpressionlevelsis,thattheyare
fundamentally important for living cells. They are dependent on the cell type,
developmental stage and influenced by environmental factors. Transcriptional
activity needs to be well-coordinated to assure the proper function of a cell.
On the other hand, a dysregulated level of transcription can lead to disease
and cancer.
To study whole genome transcription levels, microarrays have become pop-
ular in recent years. A DNA microarray can be pictured as a miniture gene-
detection assay. The detection is based on the complementary binding proper-
ties of DNA to DNA or DNA to RNA. Microarrays hold thousands of spots of
different DNA sequences each interrogating a particular gene. Different plat-
forms exist, the most common are cDNA arrays, short oligonucleotide arrays
and long oligonucleotide arrays (Figure 1).
For cDNA arrays, as used in publications 6 and 7 of this thesis, first a
library of cDNA clones, each containing the sequence of one expressed gene,
needs to be constructed. The gene sequences are amplified with PCR and
printed on a glass array. Because the size of the individual gene spots and the
amount of immobilized DNA varies between spots, usually cDNA from two
samples is labelled with different fluorescent dyes and hybridized to the same
array. Then the fluorescent signal in