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.

Babelomics contains one of the most cited tools in the field of functional enrichment analysis, the FatiGO. Two new tools have been added: Biclustering and NetworkMiner. Many other tools have been upgraded and new visualizations have been added.

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.

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.

Platform: Online tool unctional analysis.