ayout 1 - EMBL Grenoble

EMBL-EBI
The Microarray Informatics Team
Previous and current research
The Microarray Informatics team is working in four main directions:
• development of the ArrayExpress Archive and Atlas of Gene Expression;
• high-throughput data integration and analysis;
• development of algorithms for systems biology;
• biomedical informatics-related research and development projects.
Our group was among the first to use microarray data to study transcription regulation mechanisms
on a genomic scale (Brazma et al., 1998). In 1999 we realised the importance of standards
in microarray data reporting (Brazma et al., 2000, Brazma et al., 2001) and began work to establish
the ArrayExpress database. As of February 2009 the ArrayExpress Archive holds data from approximately
200,000 microarrays. The ArrayExpress Atlas of Gene Expression allows the users to
query for expression profiles of particular genes, tissues or disease states across multiple experiments.
Our PhD students and postdocs focus mostly on integrative data analysis and on building
models for systems biology (e.g., Rustici et al., 2004, Schlitt & Brazma, 2006).
Alvis Brazma
PhD 1987, Computer
Science, Moscow State
University.
Postdoctoral research in New
Mexico State University, La
Cruses.
Team leader at EMBL-EBI
since 2000.
Future projects and goals
A biological system, such as a cell, tissue, organ or organism, can be in many different states, such as developmental stages, disease states, or
physiological states. Different cell types can be considered as different biological states evolving from the progenitor cell state. This poses
many questions; how many different biological
states are there, what are the relationships between
them, which tissue or cell types are more similar to
each other and which are different, how is the biological
state affected by a disease, how much does
gene expression depends on environment, and how
much on genotype? Finding answers to these questions
is one of the most important goals of our
group’s research. Towards this goal we are building
a comprehensive gene expression atlas for human
and model organisms. The Gene Expression Atlas
integrates data from tens of thousands of transcriptomics
assays available in ArrayExpress. We
will also continue large collaborative projects, such
as integration of transcriptomics, proteomics and
human genome variation data to understand the
molecular mechanisms of disease, as well as building
biomedical data analysis infrastructure to help
us in answering these questions.
Visualisation of relationship transcriptomes of ~5,300
human samples categorised in 15 biological classes
using Neighbor Retrieval Visualizer (NeRV; Venna &
Kaski, 2007) developed by our collaborators in
Helsinki University of Technology.
Selected references
Parkinson, H. et al. (2009). ArrayExpress update – from an archive of
functional genomics experiments to the atlas of gene expression.
Nucleic Acids Res., 37, D868-872
Rustici, G. et al. (2007). Global transcriptional responses of fission
and budding yeast to changes in copper and iron levels: a
comparative study. Genome Biol., 8, R73
Schlitt, T. & Brazma, A. (2006). Modelling in molecular biology:
describing transcription regulatory networks at different scales.
Philos. Trans. R. Soc. Lond. B. Biol. Sci., 361, 83-9
Rustici, G. et al. (200). Periodic gene expression program of the
fission yeast cell cycle. Nature Genetics, 36, 809-817
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