Since its first release in 2007, GeneCodis has become a valuable tool to functionally interpret results from experimental techniques in genomics. This web-based application integrates different sources of information to finding groups of genes with similar biological meaning. This process, known as enrichment analysis, is essential in the interpretation of high-throughput experiments. The frequent feedbacks and the natural evolution of genomics and bioinformatics have allowed the growth of the tool and the development of this third release. In this version, a special effort has been made to remove noisy and redundant output from the enrichment results with the inclusion of a recently reported algorithm that summarizes significantly enriched terms and generates functionally coherent modules of genes and terms. A new comparative analysis has been added to allow the differential analysis of gene sets. To expand the scope of the application, new sources of biological information have been included, such as genetic diseases, drugs–genes interactions and Pubmed information among others. Finally, the graphic section has been renewed with the inclusion of new interactive graphics and filtering options. The application is freely available at http://genecodis.cnb.csic.es.

GeneCodis is a web server application for functional analysis of gene lists that integrates different sources of information and finds modular patterns of interrelated annotations. This integrative approach has proved to be useful for the interpretation of high-throughput experiments and therefore a new version of the system has been developed to expand its functionality and scope. GeneCodis now expands the functional information with regulatory patterns and user-defined annotations, offering the possibility of integrating all sources of information in the same analysis. Traditional singular enrichment is now permitted and more organisms and gene identifiers have been added to the database. The application has been re-engineered to improve performance, accessibility and scalability. In addition, GeneCodis can now be accessed through a public SOAP web services interface, enabling users to perform analysis from their own scripts and workflows. The application is freely available at http://genecodis.dacya.ucm.es

Babelomics is a response to the growing necessity of integrating and analyzing different types of genomic data in an environment that allows an easy functional interpretation of the results. Babelomics includes a complete suite of methods for the analysis of gene expression data that include normalization (covering most commercial platforms), pre-processing, differential gene expression (case-controls, multiclass, survival or continuous values), predictors, clustering; large-scale genotyping assays (case controls and TDTs, and allows population stratification analysis and correction). All these genomic data analysis facilities are integrated and connected to multiple options for the functional interpretation of the experiments. Different methods of functional enrichment or gene set enrichment can be used to understand the functional basis of the experiment analyzed. Many sources of biological information, which include functional (GO, KEGG, Biocarta, Reactome, etc.), regulatory (Transfac, Jaspar, ORegAnno, miRNAs, etc.), text-mining or protein–protein interaction modules can be used for this purpose. Finally a tool for the de novo functional annotation of sequences has been included in the system. This provides support for the functional analysis of non-model species. Mirrors of Babelomics or command line execution of their individual components are now possible. Babelomics is available at http://www.babelomics.org.