02142nas a2200253   4500008004100000245010200041210006900143300001100212490000700223520138600230653001501616653002401631100002401655700001801679700001601697700001401713700001501727700001601742700002001758700001501778700001701793700001501810856006301825       2008                        eng d00aBabelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments0 aBabelomics advanced functional profiling of transcriptomics prot  aW341-60 v363 a<p>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.</p>10ababelomics10afuntional profiling1 aAl-Shahrour, Fatima1 aCarbonell, J.1 aMinguez, P.1 aGoetz, S.1 aConesa, A.1 aTarraga, J.1 aMedina, Ignacio1 aAlloza, E.1 aMontaner, D.1 aDopazo, J.  uhttp://nar.oxfordjournals.org/content/36/suppl_2/W341.long