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Nucleic Acids Research Advance Access published online on May 8, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm229
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© 2007 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.

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Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite

Ramón Díaz-Uriarte1,*, Andreu Alibés1,2, Edward R. Morrissey1, Andrés Cañada1, Oscar M. Rueda1 and Mariana L. Neves1

1Statistical Computing Team, Structural and Computational Biology Programme, Spanish National Cancer Center (CNIO), Melchor Fernández Almagro 3, Madrid, 28029, Spain

*To whom correspondence should be addressed. Tel: +34 91 224 6900; Fax: +34 91 224 6972; Email: rdiaz02{at}gmail.com 2Current address: Design of Biological Systems Group, Center for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain

Received January 8, 2007. Revised March 13, 2007. Accepted March 29, 2007.

Asterias (http://www.asterias.info) is an open-source, web-based, suite for the analysis of gene expression and aCGH data. Asterias implements validated statistical methods, and most of the applications use parallel computing, which permits taking advantage of multicore CPUs and computing clusters. Access to, and further analysis of, additional biological information and annotations (PubMed references, Gene Ontology terms, KEGG and Reactome pathways) are available either for individual genes (from clickable links in tables and figures) or sets of genes. These applications cover from array normalization to imputation and preprocessing, differential gene expression analysis, class and survival prediction and aCGH analysis. The source code is available, allowing for extention and reuse of the software. The links and analysis of additional functional information, parallelization of computation and open-source availability of the code make Asterias a unique suite that can exploit features specific to web-based environments.


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