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

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.

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.long01445nas a2200253 4500008004100000245010300041210006900144300001100213490000700224520068700231653001500918653002500933100002400958700001600982700001600998700001701014700001501031700002301046700001401069700001701083700001301100700001501113856006301128 2006 eng d00aBABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments0 aBABELOMICS a systems biology perspective in the functional annot aW472-60 v343 a

We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at http://www.babelomics.org.

10ababelomics10afunctional profiling1 aAl-Shahrour, Fatima1 aMinguez, P.1 aTarraga, J.1 aMontaner, D.1 aAlloza, E.1 aVaquerizas, J., M.1 aConde, L.1 aBlaschke, C.1 aVera, J.1 aDopazo, J. uhttp://nar.oxfordjournals.org/content/34/suppl_2/W472.long02090nas a2200193 4500008004100000245012600041210006900167300001100236490000700247520144700254653001501701653002501716100002401741700001601765700002301781700001401804700001501818856006301833 2005 eng d00aBABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments0 aBABELOMICS a suite of web tools for functional annotation and an aW460-40 v333 a

We present Babelomics, a complete suite of web tools for the functional analysis of groups of genes in high-throughput experiments, which includes the use of information on Gene Ontology terms, interpro motifs, KEGG pathways, Swiss-Prot keywords, analysis of predicted transcription factor binding sites, chromosomal positions and presence in tissues with determined histological characteristics, through five integrated modules: FatiGO (fast assignment and transference of information), FatiWise, transcription factor association test, GenomeGO and tissues mining tool, respectively. Additionally, another module, FatiScan, provides a new procedure that integrates biological information in combination with experimental results in order to find groups of genes with modest but coordinate significant differential behaviour. FatiScan is highly sensitive and is capable of finding significant asymmetries in the distribution of genes of common function across a list of ordered genes even if these asymmetries were not extreme. The strong multiple-testing nature of the contrasts made by the tools is taken into account. All the tools are integrated in the gene expression analysis package GEPAS. Babelomics is the natural evolution of our tool FatiGO (which analysed almost 22,000 experiments during the last year) to include more sources on information and new modes of using it. Babelomics can be found at http://www.babelomics.org.

10ababelomics10afunctional profiling1 aAl-Shahrour, Fatima1 aMinguez, P.1 aVaquerizas, J., M.1 aConde, L.1 aDopazo, J. uhttp://nar.oxfordjournals.org/content/33/suppl_2/W460.long