Babelomics is an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. This new version of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system .

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://babelomics.bioinfo.cipf.es

In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements:

• Data input: import and quality control for the most common microarray formats
• Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent).
• Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis.
• Genotyping: stratification analysis, association, TDT.
• Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining
derived bioentities, protein-protein interaction analysis.
• Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis.

Homepage: http://babelomics.bioinfo.cipf.es