Award details

Grid Enabled Microarray Expression Profile Search

Reference	BB/D005906/1
Principal Investigator / Supervisor	Professor Richard Sinnott
Co-Investigators / Co-Supervisors	Dr Pawel Herzyk
Institution	University of Glasgow
Department	School of Computing Science
Funding type	Research
Value (£)	61,563
Status	Completed
Type	Research Grant
Start date	01/09/2005
End date	28/02/2007
Duration	18 months

Abstract

The completion of sequencing of human and several other eukaryotic genomes as well as more than hundred microbial ones mark the beginning of the post-genomic era where emphasis is shifted from searching for genes onto understanding of their function. The new discipline - functional genomics - was born and its success has been grossly facilitated by development of modern post-genomic technologies that enabled comprehensive studies of mRNA, protein and metabolite complements of biological samples. Due to the high-throughput fashion of these technologies, functional genomics has been generating large amounts of data. To be able to sensibly analyse these data well-designed data standards are required. Human Proteome Organisation's (HUPO) Proteomics Standards Initiative (PSI) [1] has adopted the PEDRO (Proteomics Experiment Data Repository) standard [2] for proteomic data. Recently, the ArMet (Architecture for Metabolomics) model was proposed for metabolomic data [3]. The most advanced work, however, has been done by the microarray community through the development of the MIAME (Minimum Information about a Microarray Experiment) standard for transcriptomic data [4]. These days leading journals require microarray data associated with publications to be MIAME compliant, and this standard has been adopted by several public data repositories. Data stored in these repositories can be easily searched using various terms belonging to carefully crafted controlled vocabularies. However, none of the existing repositories provide means for searching the deposited data by the results of a particular microarray experiment. Thus currently a researcher cannot assess if a similar experiment has been undertaken previously; if other experiments have produced similar results, or generally understand how their experiment compares to previously undertaken experiments. This proposal seeks to address this issue directly through the exploitation of Grid technology. We will extend an existing toolset from the BRIDGES project [14] with microarray experiment profile search and analysis capabilities. With this infrastructure we expect to be able to answer questions such as: 'has this microarray experiment been undertaken previously' or 'how do my microarray results compare with general public knowledge and/or with the not yet formally published data sets at collaborating site X'. Practical, Grid based solutions will be the essential yardstick upon which this project will be judged. To this end, a case study focusing upon access to and usage of microarray datasets at the Cornell University Computational Biology Service Unit, The RIKEN Genomics Science Centre in Japan and the Sir Henry Wellcome Functional Genomics Facility at Glasgow (see letters of support) will be undertaken.

Summary

The aim of this project is to develop Grid based solutions that facilitate the discovery and re-use of previously undertaken microarray experiments. In doing so, we will demonstrate the efficacy of Grid technologies for dealing with heterogeneous security infrastructures and federated microarray data environments.

Committee	Closed Committee - Engineering & Biological Systems (EBS)
Research Topics	X – not assigned to a current Research Topic
Research Priority	X – Research Priority information not available
Research Initiative	EDF (e-science Development Fund) (EDF) [2003-2005]
Funding Scheme	X – not Funded via a specific Funding Scheme

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