Standards > reporting guideline > bsg-s000168


ready Minimum Information about an ENVironmental transcriptomic experiment

Abbreviation:MIAME/Env


General Information
MIAME defines a conceptual structure for defining the core information that is common to most microarray experiments. MIAME/Env is an extension of these guidelines to cover environmental genomics.

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Record updated: Sept. 5, 2016, 9:49 a.m. by delphinedauga.




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Implementing Databases (5)
Tomato Functional Genomics Database
The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.

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.

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.

Stanford Microarray Database
The Stanford Microarray Database is a repository a microarray based gene expression and comparative genomics data. This resource is no longer being maintained please us public repositories NCBI Gene Expression Omnibus or EBI Array Express

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.

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Publications

Annotation of environmental OMICS data: application to the transcriptomics domain.

Morrison N,Wood AJ,Hancock D,Shah S,Hakes L,Gray T,Tiwari B,Kille P,Cossins A,Hegarty M,Allen MJ,Wilson WH,Olive P,Last K,Kramer C,Bailhache T,Reeves J,Pallett D,Warne J,Nashar K,Parkinson H,Sansone SA,Rocca-Serra P,Stevens R,Snape J,Brass A,Field D
OMICS 2006

View Paper (PubMed) View Paper (DOI)