Data Submission and Quality in Microarray-Based MicroRNA Profiling

Abstract

BACKGROUND Public sharing of scientific data has assumed greater importance in the omics era. Transparency is necessary for confirmation and validation, and multiple examiners aid in extracting maximal value from large data sets. Accordingly, database submission and provision of the Minimum Information About a Microarray Experiment (MIAME)3 are required by most journals as a prerequisite for review or acceptance. METHODS In this study, the level of data submission and MIAME compliance was reviewed for 127 articles that included microarray-based microRNA (miRNA) profiling and were published from July 2011 through April 2012 in the journals that published the largest number of such articles—PLOS ONE, the Journal of Biological Chemistry, Blood, and Oncogene—along with articles from 9 other journals, including Clinical Chemistry, that published smaller numbers of array-based articles. RESULTS Overall, data submission was reported at publication for <40% of all articles, and almost 75% of articles were MIAME noncompliant. On average, articles that included full data submission scored significantly higher on a quality metric than articles with limited or no data submission, and studies with adequate description of methods disproportionately included larger numbers of experimental repeats. Finally, for several articles that were not MIAME compliant, data reanalysis revealed less than complete support for the published conclusions, in 1 case leading to retraction. CONCLUSIONS These findings buttress the hypothesis that reluctance to share data is associated with low study quality and suggest that most miRNA array investigations are underpowered and/or potentially compromised by a lack of appropriate reporting and data submission.