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Chem. Res. Toxicol. 2004, 17, 2
Genomics and Proteomics The science of toxicology is continually being shaped by new technologies. In this decade, it seems clear that the marriage of genomic information with the science of toxicology will soon be complete. In some venues, this scientific crossbreeding is going under the name of “toxicogenomics”. One of the earliest results of the popularity of toxicogenomics is the emergence of microarray data to describe the influence of chemicals on biological systems. Numerous reports of such experiments are now appearing in the peer-reviewed literature, with journals springing up that are specifically directed toward publishing such work. It seems likely that hundreds, if not thousands, of reports will appear within the next few years that describe the global transcriptional changes that occur in response to a particular chemical. For simplicity, we will refer to such experiments as “chemical profiling”. In anticipation of these manuscripts, we at Chemical Research in Toxicology feel that it is important to clearly state our editorial policy toward such manuscripts, specifically those that employ microarray data sets. Two questions need to be answered; both are related to the scientific value of the data generated. First, CRT has traditionally published articles that test specific hypothesessmanuscripts that explain chemical, biochemical, or molecular mechanisms. Many microarray experiments are designed as hypothesis generating endeavors, rather than hypothesis testing ones. Should CRT publish work that only describes a response but does not explain it? Second, if one reviews the modest number of chemical profiling manuscripts that have appeared in the peerreviewed literature, a disturbing problem is evident. Journals are not requiring the underlying data to be shared with the scientific community. Very few, if any, chemical profiles provide access to the raw data that lead to the summary figures of changing global gene expression. Without such information, how can a reader appreciate the power of the data or how can the reader use such a publication in their own work? Chemical profiling by microarrays or related technologies is important. It is likely to have a significant impact on how we view chemical toxicity and will ultimately be used to understand mechanism of action. Therefore, CRT will provide a new venue for such reports in a new section called Chemical Profiles. Manuscripts submitted for consideration in this rapid publication section must adhere to a few simple rules. First, experiments must conform to the guidelines for microarray experiments as set out in the MIAME protocols (1). Second, authors of such manuscripts must agree to submit their raw data to one of two publicly accessible databases prior to publication (2, 3). Third, manuscripts must be short, with minimum speculation. We hope this new editorial policy will make Chemical Research in Toxicology a trusted and respected site for the deposition of such information. We hope this policy will serve the community of chemists and toxicologists by providing quick access to quality chemical profiles and by setting the standard for how such reports are presented and the data are shared. Relevant URLs
MGED Society: http://www.mged.org MIAME 1.1: http://www.mged.org/Workgroups/MIAME/miame_1.1.html GEO: http://www.ncbi.nlm.nih.gov/geo/ ArrayExpress: http://www.ebi.ac.uk/arrayexpress/
References (1) Brazma, A., et al. (2001) Minimum information about a microarray experiment (MIAME)stoward standards for microarray data. Nat. Genet. 29, 365-371. (2) Edgar, R., et al. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30 (1), 207-210. (3) Brazma, A., et al. (2003) ArrayExpress: a Public Repository for Microarray Gene Expression Data at the EBI (2003). Nucleic Acids Res. 31 (1), 68-71.
Chris Bradfield Associate Editor TX0342619 10.1021/tx0342619 CCC: $27.50 © 2004 American Chemical Society Published on Web 12/24/2003
