Sten Ilmjärv "Estimating differential expression from multiple indicators" | University of Tartu

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Contacts of UT units

Faculty of Arts and Humanities
Faculty phone: 
+372 737 5341
Faculty address: 
Jakobi 2, rooms 116–121, 51005 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5341
    Faculty address: 
    Jakobi 2, rooms 116–121, 51005 Tartu
  • Institute of History and Archaeology
    Faculty phone: 
    +372 737 5651
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Estonian and General Linguistics
    Faculty phone: 
    +372 737 5221
    Faculty address: 
    Jakobi 2, 51005 Tartu
  • Institute of Philosophy and Semiotics
    Faculty phone: 
    +372 737 5314
    Faculty address: 
    Jakobi 2, rooms 309–352, 51005 Tartu
  • Institute of Cultural Research
    Faculty phone: 
    (+372) 737 5223
    Faculty address: 
    Ülikooli 16, 51003 Tartu
  • School of Theology and Religious Studies
    Faculty phone: 
    +372 737 5301
    Faculty address: 
    Ülikooli 18–310, 50090 Tartu
  • College of Foreign Languages and Cultures
    Faculty address: 
    Lossi 3, 51003 Tartu
  • Viljandi Culture Academy
    Faculty phone: 
    +372 435 5232
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    Posti 1, 71004 Viljandi
Faculty of Social Sciences
Faculty phone: 
+372 737 5957
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Lossi 36, 51003 Tartu
  • Dean's Office
    Faculty phone: 
    + 372 737 5900
    Faculty address: 
    Lossi 36, 51003 Tartu
  • Institute of Education
    Faculty phone: 
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    Faculty address: 
    Salme 1a–29, 50103 Tartu
  • Johan Skytte Institute of Political Studies
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    Lossi 36–301, 51003 Tartu
  • School of Economics and Business Administration
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  • Institute of Psychology
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  • Institute of Biomedicine and Translational Medicine
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  • Institute of Pharmacy
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  • Institute of Dentistry
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  • Institute of Clinical Medicine
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    Ravila 19, 50411 Tartu
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    Faculty phone: 
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    Faculty address: 
    Jakobi 5–205, 51005 Tartu
Faculty of Science and Technology
Faculty phone: 
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Vanemuise 46–208, 51014 Tartu
  • Dean's Office
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    +372 737 5820
    Faculty address: 
    Vanemuise 46–208, 51005 Tartu
  • Institute of Computer Science
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    Faculty address: 
    Narva mnt 18, 51009 Tartu
  • Estonian Marine Institute
    Faculty phone: 
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    Faculty address: 
    Mäealuse 14, 12618 Tallinn
  • Institute of Physics
    Faculty address: 
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  • Institute of Chemistry
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    Faculty address: 
    Ravila 14a, 50411 Tartu
  • Institute of Mathematics and Statistics
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    Narva mnt 18, 51009 Tartu
  • Institute of Molecular and Cell Biology
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  • Tartu Observatory
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  • Institute of Technology
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  • Institute of Ecology and Earth Sciences
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    Vanemuise 46, 51003 Tartu
Institutions
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    +372 737 5702
    Faculty address: 
    W. Struve 1, 50091 Tartu
  • Youth Academy
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    Faculty address: 
    Uppsala 10, 51003 Tartu
  • Institute of Genomics
    Faculty phone: 
    +372 737 4000
    Faculty address: 
    Riia 23b, 51010 Tartu
  • Museum
    Faculty phone: 
    +372 737 5674
    Faculty address: 
    Lossi 25, 51003 Tartu
  • University of Tartu Natural History Museum and Botanical Garden
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    Faculty address: 
    Vanemuise 46, 51003 Tartu
Support Units
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  • Centre for Entrepreneurship and Innovation
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    Faculty address: 
    Narva mnt 18, 51009, Tartu
  • University Office in Tallinn
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    Faculty address: 
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  • Estates Office
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    Faculty address: 
    Ülikooli 18a, 51005 Tartu
  • Finance Office
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    Faculty address: 
    Jakobi 4, 51005 Tartu
  • Grant Office
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    Lossi 3, III floor, 51003 Tartu
  • Information Technology Office
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  • Marketing and Communication Office
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  • Procurement Office
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  • Rector's Strategy Office
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  • University of Tartu Press
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    Faculty address: 
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  • Tartu University Hospital
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  • University of Tartu Foundation
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  • View all other units

Sten Ilmjärv "Estimating differential expression from multiple indicators"

Date: 
24.04.2015 - 14:00

Sten Ilmjärv „Estimating differential expression from multiple indicators“

Thesis supervisor: prof Jaak Vilo, PhD, Institute of Computer Science; prof Eero Vasar, PhD, Institute of Biomedicine and Translational Medicine; Senior Research Fellow Hendrik Luuk, PhD, Institute of Biomedicine and Translational Medicine.

Oponent: Senior Research Fellow Djork-Arné Clevert, PhD, Institute of Bioinformatics, Johannes Kepler University, Linz, Austria.

Summary

With very few exceptions the genome is identical in every cell of our body. Nevertheless, our body consists of many different cells with unique shape, physiology and behavior. This variation in cell types is achieved by coordinated activity of every gene in the genome. In other words, every cell has it’s own program that regulates the activity of the genes, which subsequently determines the cell’s morphology and functionality.
 There are several technologies that can be used for measuring the activity of a gene i.e. gene expression. One of the best-known and widely used technologies is DNA-microarray developed more than two decades ago. The advantage of microarrays is that they can measure gene expression of tens of thousands of genes simultaneously. Additionally, good standards for data housing and data analysis have been established and currently the amount of microarray data in public warehouses from experiments measuring gene expression is unmatched. Therefore the reuse of available data to find answers to alternative hypothesis and the development of added-value bioinformatics tools requires flexible solutions that best exploit the potential hidden in the data.
 This work focused on developing a new framework for differential expression analysis of microarray data, termed Differential Expression from Multiple Indicators (DEMI). Our motivation was to utilize the information stored in the repeated measurements on microarrays (a gene’s expression is measured from multiple locations) to increase the sensitivity of the analysis. In comparison to other well-established methods, DEMI demonstrated a good and stable performance regardless of the microarray platform and sample size. This is especially important when samples are hard to obtain, like in clinical trials, or due to limitation in the resource, which is often the case in pilot studies. Furthermore, DEMI can handle experiments with non-conventional design, like time- or dose-dependent differential expression analysis with no replicates and identify genomic regions with unidirectional changes in gene expression levels of neighboring genes (e.g. a decrease in gene expression levels of neighboring genes can result due to large-scale epigenetic changes caused by a cancer). All in all, DEMI provides a flexible solution for differential expression analysis and is able to answer new questions from already published data.

Organizer: 
Tuuli Ruus
Location: 
Ravila 19 ˗ 1006
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