standards > reporting guideline > DOI:10.25504/FAIRsharing.32b10v


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ready Minimum Information About a Microarray Experiment

Abbreviation: MIAME


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General Information
MIAME is intended to specify all the information necessary for an unambiguous interpretation of a microarray experiment, and potentially to reproduce it. MIAME defines the content but not the format for this information.


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How to cite this record FAIRsharing.org: MIAME; Minimum Information About a Microarray Experiment; DOI: https://doi.org/10.25504/FAIRsharing.32b10v; Last edited: July 24, 2018, 10:30 a.m.; Last accessed: Nov 14 2018 9:38 p.m.


Record updated: July 24, 2018, 10:30 a.m. by The FAIRsharing Team.

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Publications

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Brazma A,Hingamp P,Quackenbush J,Sherlock G,Spellman P,Stoeckert C,Aach J,Ansorge W,Ball CA,Causton HC,Gaasterland T,Glenisson P,Holstege FC,Kim IF,Markowitz V,Matese JC,Parkinson H,Robinson A,Sarkans U,Schulze-Kremer S,Stewart J,Taylor R,Vilo J,Vingron M
Nat Genet 2001

View Paper (PubMed) View Publication

Minimum Information About a Microarray Experiment (MIAME)--successes, failures, challenges.

Brazma A
ScientificWorldJournal 2009

View Paper (PubMed) View Publication


Implementing Databases (10)
BuG@Sbase
BuG@Sbase is a microbial gene expression and comparative genomic database containing microarray datasets.

ArrayExpress
ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database.

GermOnline
GermOnline is a cross-species database gateway focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome.

Gene Expression Omnibus
The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the studies and gene expression patterns stored in GEO.

Chemical Effects in Biological Systems (CEBS)
CEBS (Chemical Effects in Biological Systems) is an integrated public repository for toxicogenomics data, including the study design and timeline, clinical chemistry and histopathology findings and microarray and proteomics data. CEBS contains data derived from studies of chemicals and of genetic alterations, and is compatible with clinical and environmental studies. CEBS is designed to permit the user to query the data using the study conditions, the subject responses and then, having identified an appropriate set of subjects, to move to the microarray module of CEBS to carry out gene signature and pathway analysis.

Cancer Genome Mine
Clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.

Immunology Database and Analysis Portal
The ImmPort system serves as a long-term, sustainable archive of immunology research data generated by investigators mainly funded through the NIAID/DAIT. The core component of the ImmPort system is an extensive data warehouse containing an integration of experimental data and clinical trial data. The analytical tools created and integrated as part of the ImmPort system are available to any researcher within ImmPort after registration and approval by DAIT. Additionally, the data provided mainly by NIAID/DAIT funded researchers in ImmPort will be available to all registered users after the appropriate embargo time. ImmPort, is the data submission portal where researchers upload, QC, and curate their data prior to sharing in OpenImmPort.

Interferome
This database enables the reliable identification of an individual Interferon Regulated Gene (IRG) or IRG signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It also assists in identifying regulatory elements, chromosomal location and tissue expression of IRGs in human and mouse. This upgraded version, Interferome v2.0 has quantitative data, more detailed annotation and search capabilities and can be queried for one to a thousand genes, such as from from a microarray experiment.

Longhorn Array Database
The Longhorn Array Database (LAD) is a MIAME‐compliant microarray database that operates on PostgreSQL and Linux. It is a free, completely open‐source, and provides a systematic and proven environment in which vast experiment sets can be safely archived, securely accessed, biologically annotated, quantitatively analyzed, and visually explored. This unit provides the complete set of information needed to successfully deploy, configure, and use LAD for the purposes of two‐color DNA microarray analysis and visualization.

BarleyBase
BarleyBase is a public data resource of Affymetrix GeneChip data for plants.

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