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Bioinformatics Advance Access originally published online on July 9, 2009
Bioinformatics 2009 25(19):2566-2572; doi:10.1093/bioinformatics/btp422
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

aGEM: an integrative system for analyzing spatial-temporal gene-expression information

Natalia Jiménez-Lozano *,{dagger}, Joan Segura {dagger}, José Ramón Macías , Juanjo Vega and José María Carazo

GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit of the National Centre for Biotechnology (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain

*To whom correspondence should be addressed.


  Abstract

Motivation: The work presented here describes the ‘anatomical Gene-Expression Mapping (aGEM)’ Platform, a development conceived to integrate phenotypic information with the spatial and temporal distributions of genes expressed in the mouse. The aGEM Platform has been built by extending the Distributed Annotation System (DAS) protocol, which was originally designed to share genome annotations over the WWW. DAS is a client-server system in which a single client integrates information from multiple distributed servers.

Results: The aGEM Platform provides information to answer three main questions. (i) Which genes are expressed in a given mouse anatomical component? (ii) In which mouse anatomical structures are a given gene or set of genes expressed? And (iii) is there any correlation among these findings? Currently, this Platform includes several well-known mouse resources (EMAGE, GXD and GENSAT), hosting gene-expression data mostly obtained from in situ techniques together with a broad set of image-derived annotations.

Availability: The Platform is optimized for Firefox 3.0 and it is accessed through a friendly and intuitive display: http://agem.cnb.csic.es

Contact: natalia{at}cnb.csic.es

Supplementary information: Supplementary data are available at http://bioweb.cnb.csic.es/VisualOmics/aGEM/home.html and http://bioweb.cnb.csic.es/VisualOmics/index_VO.html and Bioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First authors.

Associate Editor: David Rocke

Received on October 20, 2008; revised on July 7, 2009; accepted on July 7, 2009

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