2/2013

ESTOOLS DATA@HAND opens up new avenues in stem cell research

 


“Genome-wide expression data of stem cells is now available to all researchers. ESTOOLS
DATA@HAND offers user-friendly data integration and analysis tools, stores research
materials for future reference and enables comparative studies,” say Lingjia Kong, Reija
Autio, Kirsi Granberg and Kaisa-Leena Aho.

Scientists are now better equipped to understand stem cells and the behaviour of their genes. The unique “fingerprints” of stem cells are stored in a recently launched global database in a bid to speed up stem cell research and develop, for example, new stem cell-based treatments.   

Stem cells are the focus of intense scientific interest among biomedical researchers. Stem cell research holds great promise for understanding genetic disease mechanisms, developing new treatments and even repairing damaged tissue. Stem cell therapy offers new hope for people suffering from currently incurable neurodegenerative diseases, such as Parkinson’s or Alzheimer’s, or different forms of heart disease.

Rebuild your bones

Since it is important to examine all the genes expressed in a particular stem cell line in specific conditions, researchers use microarrays that allow the simultaneous measurement of the gene expressions of all ~20,000 genes within a single human cell.

“Microarray data resembles a fingerprint that uniquely identifies each cell and provides a snapshot of their characteristics,” says Kaisa-Leena Aho.

Aho’s doctoral dissertation, approved at Tampere University of Technology in autumn 2013, explored gene expression in stem cells derived from human adipose tissue and their potential to enhance bone regeneration. Stem cells were cultured under conditions that meet the requirements of clinical application. These findings provide new insights into gene expression and contribute to the global efforts to increase the safety of stem cell therapies.  

“Adipose-derived stem cells have been differentiated, among others, into osteoblasts under laboratory conditions and further used to rebuild bone tissue ravaged by cancer,” says Aho.

One-stop repository for stem cell data

Researchers from all over the world analyse gene expressions using microarrays. However, the number of samples tends to be limited due to the relatively expensive costs of microarrays. Although researchers may routinely store their data in international open-access repositories, their results are not conveniently available to others, because the integration and analysis of the data often requires programming skills. It has also been difficult to compare the research carried out in different countries and by different research groups.

The challenge to promote the availability and comparability of stem cell data was taken on by the Computational Systems Biology (CSB) research group headed by Professor Olli Yli-Harja at TUT.  

“We collected and pre-processed existing measurement data and developed computational tools to enable scientists to effectively and conveniently analyse and manage massive amounts of data.  The result is the largest currently available database that facilitates the exploration of gene expression array data in stem cell research,” says Lingjia Kong.

Kong’s doctoral dissertation summarizes the state of the art of gene expression data analysis, with particular focus on the construction of database applications geared towards the integration of gene expression microarray data (the ESTOOLS DATA@HAND resource is one of the database applications). The ability to integrate existing data will provide enormous opportunities in deciphering molecular mechanisms underlying biological studies, since it allows previously published data to yield novel scientific discoveries.

CSB’s project was coordinated by DTech Reija Autio at TUT. The project also involved, among others, researchers Lingjia Kong, Kirsi Granberg, Kaisa-Leena Aho and Christophe Roos, who bore the primary responsibility for developing the database and user interface and for collecting and analysing the samples. The system was developed in collaboration with Professor Riitta Lahesmaa’s research group at Turku Centre of Biotechnology and Professor Peter Andrews’s group at the University of Sheffield. The project was part of the European ESTOOLS consortium that brings together the combined expertise of 21 universities and research centres. The CSB group joined the consortium in 2008.

The research results were published in the September 2013 issue of the acclaimed scientific journal Nature Methods.

CSB’s dedication to the analysis of complex biological phenomena has spawned not only publications and dissertations but also spin-offs, such as Bioptima Ltd, Euformatics Ltd, Genevia Ltd and Quva Ltd.

 

New database facilitates stem cell research

The ESTOOLS DATA@HAND resource contains human gene expression array data from more than 70 sample sets and around 1,200 arrays. The data was retrieved from publicly accessible online repositories. Each sample comprises gene expression measurements of around 20,000 human genes. Detailed information on the cell type, processing and source of each sample was deposited in the database to ensure optimal usability of the data.  The online resource offers access to a wealth of measurement data and provides diagrams and tools for easy visualization, computational analysis and cross-study comparisons.

Link to the database: http://estools.cs.tut.fi/

 

Text: Marjut Kemiläinen
Photo: Virpi Andersin

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