01445nas 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<p>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.</p>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<p>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.</p>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