Microarray data repository

This section describes the use of the microarray technology for transcriptional profiling. The section includes a summary of the experimental procedures (section on Experimental design), the most widely used array platforms (section on Platforms for Gene Expression Analysis), and briefly summarizes the data analysis steps, the software that can be used, and the public microarray data repositories (sections on Analysis of microarray data and Data sharing). 

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. 

Microarray databases are repositories containing experimental microarray data, mainly microarray gene expression data. Microarray databases are used to store the results of finished experiments, and to make the data available to other users and applications, either directly or via user download. Microarray databases can fall into two distinct classes ... 

The importance acquired by the microarray technology and its input to the research community can be illustrated by browsing at the best-known expression data repository, the Gene Expression Omnibus (GEO http //www.ncbi. nlm.nih.gov/geo/) (28). For example, in mid-2013 the array model Human Genome U133 Plus 2.0 of Asymetrix (entry GPL570) accounts for 82,767 hybridized samples, distributed by 3093 data series. 

There are currently no publicly available DNA chip expression databases, however the Microarray Gene Expression Database Group (MGED) [3] at the EBI aims to facilitate the creation of a gene expression data repository. 

Although compliance with MGED guidelines is still somewhat limited, it is of note that journals such as Nature, Cell, and The Lancet have adopted these guidelines for submitting microarray expression data for publication. In addition to demanding MIAME-compliant data, Nature and Cell require authors to submit their microarray data to a public repository as a precondition... 

Waters, M., Stasiewicz, S., and Merrick, B. A. 2008. CEBS—Chemical effects in biological systems A public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Res. 36 D892-D900. 

GEO Gene Expression Data repository for microarrays from all organ- www.ncbi.nlm.nih. 

ArrayExpress Ovb Data repository from all organisms, visualization of expression in individual data sets www.ebi.ac.uk/ microarray-as/aer... 

Public repositories of microarray gene expression data have been developed to store the results of array experiments ArrayExpress (32) in Europe, Gene Expression Omnibus (GEO) in the United States (33), and the Center for Information Biology Gene Expression Database (CIBEX) (34) in Japan. Many journals already require an accession number (indicating that a data set has been submitted to one of these public databases) prior to publication. 

Brazma A, Parkinson HS, Sarkans U et al. ArrayExpress a publie repository for microarray gene expression data at the EBl. Nucleic Acids Res 2003 31 68-71. 

Gene expression profiling is an approach to identify dys-regulated genes in response to drug treatment. Data are available through public repositories, the Gene Expression Omnibus at NIH (http //www.ncbi.nlm.nih.gov/geo/) and the ArrayEx-press at EBI (http //www.ebi.ac.uk/microarray-as/ae/). 

Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA. ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003 31 68-71. 

The European Bioinformatics Institute (EBI). This site is located at Hinxton Hall, Cambridge, UK. The home of the EMBL Nucleotide Sequence Database data management tools [including publicly accessible version of SRS—the Sequence Retrieval System (7)] protein family databases microarray tools etc. An extensive repository of resources for bioinformatics. 

Those two efforts together contributed to a number of scientific journals that require MIAME-comphant data as a condition for publishing microarray-based articles. This implies appropriate description of the data and submission of the raw data to one of the existing public repositories, which has made the microarray field much more transparent than others where, for instance, data still are kept by the authors of the studies. 

Parkinson, H., Sarkans, U., Shojatalab, M., Abeygunawardena, N., Contrino, S., Coulson, R., Fame, A., Lara, G.G., Holloway, E., Kapushesky, M., et al. 2005. ArrayExpress—a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 33 D553-555. 

MIAME, (minimal information about a microarray experiment), a set of guidelines about experimental annotation aimed at developing microarray repositories and data analysis tools www.mged.org/Workgroups/MIAME/miame.html. 

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