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Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement 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 display.


Keywords

gene, anatomy, gene expression, anatomical structure, developmental stage, functional genomics, genomics

Resource ID

SCR_013349

Alternate IDs

nlx_152022

Website Status

Last checked down

Abbreviation(s)

aGEM

Species

human, mouse

Resource Type

Resource, data or information resource, database

Funding Information

National Institute for Bioinformatics, AMIT Programme CDTI | CEN-20101014, RESOLVE | UE CE:FP7-202047, Ministerio de Ciencia e Innovacion | BIO2010-16566, Biostruct-X | FP7-Infrastructures-2011-1, Centrosoma 3D | CSD2006-00023

Synonym(s)

anatomic Gene Expression Mapping

Proper citation

(aGEM, RRID:SCR_013349)

Reference

PMID:22106336

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Integrating human and murine anatomical gene expression data for improved comparisons.

  • JimĂ©nez-Lozano N
  • Bioinformatics
  • 2012 Feb 1

MOTIVATION: Information concerning the gene expression pattern in four dimensions (species, genes, anatomy and developmental stage) is crucial for unraveling the roles of genes through time. There are a variety of anatomical gene expression databases, but extracting information from them can be hampered by their diversity and heterogeneity. RESULTS: aGEM 3.1 (anatomic Gene Expression Mapping) addresses the issues of diversity and heterogeneity of anatomical gene expression databases by integrating six mouse gene expression resources (EMAGE, GXD, GENSAT, Allen Brain Atlas data base, EUREXPRESS and BioGPS) and three human gene expression databases (HUDSEN, Human Protein Atlas and BioGPS). Furthermore, aGEM 3.1 provides new cross analysis tools to bridge these resources. AVAILABILITY AND IMPLEMENTATION: aGEM 3.1 can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. http://agem.cnb.csic.es CONTACT: natalia@cnb.csic.es SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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