EMAGE is an online biological database

Biological database

Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analyses. They contain information from research areas including genomics, proteomics, metabolomics, microarray...

 of gene expression

Gene expression

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...

 data in the developing mouse (Mus musculus) embryo. The data held in EMAGE is spatially annotated to a framework of 3D mouse embryo models produced by EMAP (e-Mouse Atlas Project). These spatial annotations allow users to query EMAGE by spatial pattern as well as by gene name, anatomy term or Gene Ontology (GO)

Gene Ontology

The Gene Ontology, or GO, is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species...

 term. EMAGE is a freely available web-based resource funded by the Medical Research Council (UK)

Medical Research Council (UK)

The Medical Research Council is a publicly-funded agency responsible for co-ordinating and funding medical research in the United Kingdom. It is one of seven Research Councils in the UK and is answerable to, although politically independent from, the Department for Business, Innovation and Skills...

 and based at the MRC Human Genetics Unit

MRC Human Genetics Unit

The Medical Research Council Human Genetics Unit is situated at the Western General Hospital in Edinburgh. It is one of the largest MRC research establishments, housing over two hundred scientists, support staff, research fellows, PhD students, and visiting workers.-Directors:* 1956 - 1969 Dr...

 in the Institute of Genetics and Molecular Medicine, Edinburgh, UK.

Contents

EMAGE contains in situ hybridisation

In situ hybridization

In situ hybridization is a type of hybridization that uses a labeled complementary DNA or RNA strand to localize a specific DNA or RNA sequence in a portion or section of tissue , or, if the tissue is small enough , in the entire tissue...

, immunohistochemistry

Immunohistochemistry

Immunohistochemistry or IHC refers to the process of detecting antigens in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues. IHC takes its name from the roots "immuno," in reference to antibodies used in the procedure, and...

, and in situ reporter (e.g. knock-in

Gene knockin

In molecular cloning and biology, a Knock-in refers to a genetic engineering method that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because...

 and gene trap

Gene trapping

Gene trapping is a high-throughput approach that is used to introduce insertional mutations across the mammalian genome. It is performed with gene trap vectors whose principal element is a gene trapping cassette consisting of a promoterless reporter gene and/or selectable genetic marker flanked by...

) data. It includes wholemount data, section

Histological section

Histological section refers to thin slices of tissue applied to a microscopic slide, usually around 5 to 10 micrometres thick, which are viewed under a microscope...

 data and full 3D OPT (Optical Projection Tomography

Optical projection tomography

Optical projection tomography is a form of tomography involving optical microscopy.It is in many ways the optical equivalent of X-Ray Computed Tomography or the medical CT scan. OPT differs in the way that it assumes parallel ray projection as opposed to fan beam projection as is the case for X-ray...

) data. The gene expression patterns are mapped into or onto the standard models by a team of biocurators

Biocurator

A biocurator is a professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases...

, using bespoke mapping software. In addition to the spatial annotations, EMAGE data is also text annotated to provide a text based description of the expression patterns. This text annotation is carried out in collaboration with the MGI Gene Expression Database (GXD) using the EMAP mouse anatomy ontology.

EMAGE data comes primarily from peer reviewed, published journal articles, and from large scale screens, but also from direct submissions from researches working in the field. Data does not need to be published to be included in EMAGE, however EMAGE is a curated database. Biocurators check the accuracy of the meta-data included in the database entries and as well as performing the spatial annotations of the data.

EMAGE entries are designed to adhere to the Minimum information specification

Minimum Information Standards

Minimum Information standards or reporting guidelines specify the minimum amount of meta data and data required to meet a specific aim or aims. Usually the aim is to provide enough meta data and data to enable the unambiguous reproduction and interpretation of an experiment...

for in situ hybridization and immunohistochemistry experiments (MISFISHIE) specifications, and as such contain information about the submitter/author publication, detection reagent, assay specimen preparation, and experimental procedures as well as the original data images and the spatial and text annotations. EMAGE entries also contain links to a variety of related resources based on the either the gene being assayed, or the assay itself.