Minimum Information About a Microarray Experiment (MIAME) – Successes, Failures, Challenges

The Minimum Information About a Microarray Experiment (known as MIAME) guidelines describe information that needs to be provided to enable the interpretation of the results of a microarray-based experiment unambiguously. The MIAME guidelines were developed by the Microarray Gene Expression Data (MGED) Society. Since the MIAME position paper was published in 2001, it has been cited in the scientific literature well over a thousand times. MIAME has been replicated for many other technologies, the major data repositories are supporting MIAME, and most scientific journals have adopted MIAME guidelines as a requirement for publishing. With the advent of new-generation sequencing technology, MIAME faces new challenges. To address this, the MGED Society has proposed new guidelines, i.e., Minimum Information about a high-throughput SeQuencing Experiment (MINSEQE). Here we present analysis of the reasons for the success of MIAME, as well as discuss where it has failed, and the challenges it faces.

[1]  Jason E. Stewart,et al.  Design and implementation of microarray gene expression markup language (MAGE-ML) , 2002, Genome Biology.

[2]  Ibrahim Emam,et al.  ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression , 2008, Nucleic Acids Res..

[3]  Nigel W. Hardy,et al.  The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?". , 2008, Omics : a journal of integrative biology.

[4]  Kazuho Ikeo,et al.  CIBEX: center for information biology gene expression database. , 2003, Comptes rendus biologies.

[5]  P. Zimmermann,et al.  GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox1[w] , 2004, Plant Physiology.

[6]  Nigel W. Hardy,et al.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.

[7]  C. Ball,et al.  Repeatability of published microarray gene expression analyses , 2009, Nature Genetics.

[8]  A. Brazma,et al.  Standards for systems biology , 2006, Nature Reviews Genetics.

[9]  Duccio Cavalieri,et al.  Standards for Microarray Data , 2002, Science.

[10]  T. Barrette,et al.  ONCOMINE: a cancer microarray database and integrated data-mining platform. , 2004, Neoplasia.

[11]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[12]  Paul T. Spellman,et al.  A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB , 2006, BMC Bioinformatics.

[13]  Heather A. Piwowar,et al.  Sharing Detailed Research Data Is Associated with Increased Citation Rate , 2007, PloS one.

[14]  Helen Parkinson,et al.  ArrayExpress service for reviewers/editors of DNA microarray papers , 2006, Nature Biotechnology.

[15]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[16]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..