Large DNA microarray dataset is made publicly available by LGC and the European Bioinformatics Institute (EBI)

As the next phase of DTI’s Measurements for Biotechnology (MfB) programme to 2007 gets underway, a large DNA microarray dataset generated by an LGC-led consortium during the first phase is now freely available online at ArrayExpress, a leading public repository managed by the European Bioinformatics Institute (EBI). The sharing of well-annotated data is a primary objective of the Microarray Gene Expression Data (MGED) Society and this repository is stored in accordance with MGED recommendations.

Since the mid-1990s, DNA microarray technology has developed into a major tool for the investigation of global gene expression for all aspects of human disease. The technology is currently being explored for its efficacy in genomic approaches to toxicology. As toxicity is still the major cause of failure in clinical trials, there is strong industry interest in improved models for predictive toxicology.

Dr Carole Foy of LGC’s Bio-Molecular Innovation group said: “This dataset is a significant milestone from the MfB project, ‘Comparability of gene expression measurements,’ completed in 2004. It is a tribute to everyone involved in the consortium – NPL, Human Genome Mapping Project, Oxford Biomedica, Renovo and Royal London Hospital – that other scientists and analysts can now access this valuable data.

“So that the performance of microarrays can be maximised, LGC is working with the EBI in the current MfB programme on the project, ‘Toxicogenomics: Quality metrics for improving microarray based measurements,’ under the new Gene Measurement theme,” she added.

The dataset produced by the LGC-led consortium relates to four commercially available arrays that probe the human genome, with between 4,000 and 30,000 genes probed per array. LGC measured gene expression status on 24 replicate arrays for each manufacturer, comparing a brain sample to a universal reference sample. NPL then contributed to the subsequent data analysis and normalisation in which nearly 700 text files containing well over eight million rows of microarray data were created. The dataset can be accessed at www.ebi.ac.uk/arrayexpress.