Microarray gene data should be made public

Related tags Gene expression Dna Molecular biology

A team of researchers has issued a plea that that
microarray-derived gene expression data should be available in a
public repository in the same way that gene sequence data is
collated for use by all.

The researchers are all part of the Microarray Gene Expression Data Society​, and they make their case in the latest issue of PloS Biology​.

"A fundamental principle guiding the publication of scientific results is that the data supporting any scholarly work must be made fully available to the research community, [and] in the context of molecular biology, this has typically meant that authors of a paper describing a newly sequenced genome, gene, or protein must deposit the primary data in a permanent, public data repository,"​ they note.

At present, a great deal of this data is residing on individual authors' websites in a variety of formats, so it is lost to the usual scientific practice of peer-review and appraisal to gauge its accuracy and relevance.

The MGED maintains that it is now becoming feasible to organise this data, just as gene sequences are organised in databases maintained by the DNA Data Bank of Japan (DDBJ), European Bioinformatics Institute (EBI), and National Center for Biotechnology Information (NCBI).

"All scholarly scientific journals should now require the submission of microarray data to public repositories as part of the process of publication,"​ according to the group. Some journals have already made this a condition of acceptance, but submission requirements need to be applied consistently.

To that end, they recommend that various databases - ArrayExpress, Gene Expression Omnibus, and the Centre for Information Biology Gene Expression Database (CIBEX) - can serve as acceptable public repositories.

Adopting this approach will provide some assurance that published gene expression datasets will continue to be available into the future. In addition, having the data will allow expression data to be integrated with other relevant data, such as genome sequences, single nucleotide polymorphism (SNP) and haplotype mapping information that can help scientists interpret expression patterns.

The MGED was set up in 1999 and is behind the MIAME (minimum information about a microarray experiment) guidelines for the annotation of microarray data.

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