MIAME experiment

Abbreviation Bp, nucleotide base pairs cDNA, complementary DNA ChIP, chromatin Immunoprecipi-tation Cy5, cyanine 5-dCTP Cy3, cyanine 3-dCTP ESTs, expressed sequence tags FDR, false discovery rate MIAME, minimum information about a microarray experiment mRNA, RNA, messenger NIA, National Institutes of Aging RFUs, relative fluorescence units RT-PCR, reverse transcriptase polymerase chain reaction SAGE, serial analysis of gene expression SAM, significance analysis of microarrays... 

Although microarray experiments generate vast amounts of data, typically, the experimental question can be answered with only a small fraction of this information. By sharing complete datasets with the research community (published results or results that will not be published) the full utility of microarray results can be realized. By conforming to the MIAME standards, microarray data become more interpretable and extensible. 

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, et al. 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 29 365. 

Figure 1.16 Critical issues facing DNA microarrays and protein microarrays. MIAME = minimum information about a microarray experiment, checklist endorsement as of October 14, 2002. RCA = rolling circle amplification. RLS = resonance light scattering.

To make full use of microarray data it is necessary that data of published microarray experiments be made available to other researchers for comparison purposes. To this end, the Minimum Information About a Microarray Experiment (MIAME) (31) guidelines have been developed at the European Bioinformatics Institute (EBI). This standard describes the minimum information required to ensure that microarray data can be easily interpreted, and that results derived from its analysis can be independently verified. 

This section will discuss the standards for sharing and discussing microarray experiments, including the ontologies and controlled vocabularies. A non-technical description of the sharing process will be provided, as well as an introduction to the pharmacology/toxicology focused version of the MIAME standard, MIAME/Tox, which is currently under development. 

The MIAME standard defines the minimum information investigators must report for a microarray experiment to be reproduced. The MAGE standard was born partially from MIAME, and the European Bioinformatics Institute used MIAME and MAGE to guide the development of ArrayEx-press, their public genomic data repository (34). Sample annotation lies at the heart of MIAME, underscoring the need to understand as completely as possible the experimental conditions that may influence the microarray data. Many journals that publish microarray data require the submission of MIAME-supportive microarray data to a public genomic data repository as a condition of publication. These typically include submission of protocols species, strains, and sex used for in vivo studies cell line name and culture conditions for in vitro studies, and other relevant information. 

MIAME Minimum information about a microarray experiment... 

The Microarray Gene Expression Data Society created the MIAME (Minimum Information About a Microarray Experiment) standards for the description of microarray experiments and for the exchange of microarray data. 

The MIAME standard was created by the Functional Genomics Data Society, formerly known as the Microarray Gene Expression Data Society (http // www.mged.org), as an effort to provide standards to specify all the information necessary to describe and interpret unambiguously the results of a microarray experiment (74). The standard defines the contents required for compliance reports but it does not specify the format in which this data should be presented. As a consequence there are a number of different file formats for representing this data, and each public and subscription database has adopted its own format. 

Minimum Information About a Microarray Experiment (MIAME) for Toxicogenomics, European Bioinformatics Institute, National Center for Toxicogenomics, International... 

It is important that all the information that may be needed to interpret the results of a microarray experiment at a later date, and possibly to verify the experiment, is captured and recorded in the database. The microarray data annotations working-group of MGED has developed a list of requirements that have to be satisfied to meet these goals, called the Minimum Information About a Microarray Experiment (MIAME). 

We recommend that all the information about microarray experiments specified in MIAME is captured by the users in a database. The database design described below can be used to satisfy the MIAME requirements. 

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., et al. 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29 365-371. 

Minimum Information About a Microarray Experiment (MIAME, http // www.mged.org/miame) is a document that describes the minimum information required to ensure easy interpretation and independent verification of microarray data [55]. A guideline itemizes the detailed information that should be included while reporting a microarray experiment (see Table 18.1-1 for a summarized checklist). 

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