anatomic Gene Expression Mapping Platform (aGEM)

Category Genomics>Gene Expression Analysis/Profiling/Tools

Abstract The aGEM Platform is an integrative system for analyzing spatial-temporal gene expression information.

This advanced platform makes it easy to access information related to the 'anatomical pattern' of 'gene expression' in the mouse, so that it can be used in many functional genomics studies.

The platform allows the integration of gene expression data with spatial- temporal anatomic data by means of an intuitive and user friendly viewer.

The aGEM Platform has been built by extending the Distributed Annotation System (DAS) protocol that was originally designed to share ‘genome annotations’ over the World Wide Web (WWW).

DAS is a client-server system in which a single client integrates information from multiple distributed servers.

The aGEM Platform provides information to answer three (3) main questions:

1) Which are the genes that are expressed in a given anatomical component?

2) In which anatomical structures are a given gene (or set of genes) expressed?

3) Is there any correlation among these findings?

Currently this Platform includes several well-known mouse resources (EMAGE, GXD, GENSAT, ABA and Symatlas), hosting gene expression data obtained mostly from 'in situ' techniques together with a broad set of image derived annotations, and general biological information databases such as KEGG and OMIM.

aGEM Not only gives an integrated view of the databases mentioned above, but also allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time).

Overview of integrated aGEM databases --

1) The EMAGE database was the result of an innovative project that started in 1994, the UK MRC Human Genetics Unit in Edinburgh, together with the Jackson Laboratory in the USA (Ringwald M. et al, 1994).

This project was devoted to create 3D grey-level voxel images from several mouse developmental stages (named Theiler Stages) on which image-mapped gene-expression data coming from in situ experiments were referred (EMAGE database, Venkataraman S. et al, 2008).

2) The GXD database is a component of the Mouse Genome Informatics (MGI) resource, the community model organism database for the laboratory mouse.

GXD currently stores gene expression data coming from in situ techniques as well as from other techniques such as northern blot, real- time polymerase chain reaction, etc, and referring to the embryo and adult mouse.

3) The GENSAT project aims to map the expression of genes in the central nervous system (CNS) of the mouse, using both in situ hybridization and transgenic mouse techniques. It is a collection of pictorial gene expression maps of the brain and spinal cord of the mouse.

GENSAT catalogs images of histological sections of the developing (embryonic days 10.5 and 15.5) and adult mouse brain in which tags, such as ‘Enhanced Green Fluorescence Protein’, have been used to visualize the relative degree in situ expression for a wide array of genes.

Please note that currently this database includes only data for the Theiler stages 16, and 23 plus the adult mouse.

4) The Allen Brain Atlas (ABA), which is the result of a project that systematically profiles 3D high-resolution gene expression in postnatal mouse brains for thousands of genes by performing in situ hybridization in an automated fashion.

5) GNF-Symatlas, which is an atlas of gene expression in 79 human and 61 mouse tissues obtained by means of microarray technology.

6) The Mouse Tumor Biology Database (MTB) provides access to data about endogenously arising tumors in genetically defined mice.

7) The Online Mendelian Inheritance in Man (OMIM) database is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes.

The full-text, referenced overviews in OMIM contain information on all known Mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.

8) The KEGG Pathway database is a collection of pathway maps representing knowledge on the molecular interaction and reaction networks for metabolism, genetic information processing, environmental information processing, cellular processes, human diseases and drug development images from several mouse developmental stages (named Theiler Stages) on which image- mapped gene-expression data coming from in situ experiments were referred (EMAGE database, Venkataraman S. et al, 2008).

OWLViewer --

To make the 'query by anatomy' easier, in aGEM v2.0 the manufacturer has included an advanced and friendly ontology viewer.

If the user knows the exact name of the anatomical component they want to search for, the viewer will find it in the broad ontology.

On the other hand, the viewer has an 'auto-complete function' that helps the user if they do Not know the exact name of the anatomical structure.

OWLViewer allows you to explore a wide set of OWL ontology files, like the developmental mouse anatomical ontology (EMAP), displaying the terms and relations between them.

OWLViewer is also integrated with the Visual Genomics platform aGEM, allowing you to search for additional info related to anatomical terms.

OWLViewer has been created using Java technology, to provide a widely available environment using third-party libraries like ‘prefuse’ or the OWL-API.

The application can also be used via web browsers due to Java Web Start technology, without explicit installation or download.

OwlViewer main features/capabilities include:

1) Ontology files can be loaded automatically at start up using application parameters. Also a term can be displayed automatically using the same mechanism.

2) If provided within the ‘ontology file’, additional info (definition, author or comments) is displayed when you mouse over a node to help you with the identification of terms.

3) Allows searching in the ontology tree, expanding the desired term, providing its name or identifier, including auto-complete functionality.

4) Provides ‘cache’ support to minimize network traffic.

5) Allows you to save 'the ontology' in graphical or comma separated values (CVS) format.

System Requirements

Web-based.

Manufacturer

Manufacturer Web Site aGEM OwlViewer

Price Contact manufacturer.

G6G Abstract Number 20476

G6G Manufacturer Number 104101