Integrating human and murine anatomical gene expression data for improved comparisons

• Published in: Bioinformatics Vol. 28; no. 3; pp. 397 - 402
• Main Authors: Jiménez-Lozano, Natalia, Segura, Joan, Macías, José Ramón, Vega, Juanjo, Carazo, José María
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.02.2012
• Subjects: Algorithms; Animals; Biological and medical sciences; Brain - metabolism; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; Gene Expression Regulation, Developmental; General aspects; Humans; Huntington Disease - genetics; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Mice; Organ Specificity; Human; Vertebrata; Mammalia; Gene; Mouse; Rodentia; Data; Gene expression
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btr639

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.