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Nucleic Acids Research Advance Access originally published online on May 31, 2008
Nucleic Acids Research 2008 36(Web Server issue):W341-W346; doi:10.1093/nar/gkn318
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W341-W346
© 2008 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.

Articles

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments

Fátima Al-Shahrour1, José Carbonell1, Pablo Minguez1,2, Stefan Goetz1,2, Ana Conesa1, Joaquín Tárraga1,3, Ignacio Medina1,2, Eva Alloza1, David Montaner1,3 and Joaquín Dopazo1,2,3,*

1Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Autopista del Saler 16, E46013 Valencia, 2CIBER de Enfermedades Raras (CIBERER), Valencia, E46013 and 3Functional Genomics Node, INB, CIPF, Valencia, E46013, Spain

*To whom correspondence should be addressed. Tel: +34 96 328 96 80; Fax: +34 96 328 97 01; Email: jdopazo{at}cipf.es

Received January 31, 2008. Revised April 19, 2008. Accepted May 7, 2008.

We present a new version of Babelomics, a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available. In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules. Finally, a tool for the ‘de novo’ functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org


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