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Nucleic Acids Research 2005 33(Web Server Issue):W460-W464; doi:10.1093/nar/gki456
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments

Fátima Al-Shahrour1, Pablo Minguez1, Juan M. Vaquerizas1, Lucía Conde1 and Joaquín Dopazo1,2,*

1Bioinformatics Unit, Centro Nacional de Investigaciones Oncológicas (CNIO) Melchor Fernández Almagro 3, 28029, Madrid, Spain 2Functional Genomics Node, INB, Centro de Investigación Príncipe Felipe Autopista del Saler 16, E46013, Valencia, Spain

*To whom correspondence should be addressed. Tel: +34 96 3289680; Fax: +34 96 3289701; Email: jdopazo{at}cnio.es

Received February 14, 2005. Revised April 4, 2005. Accepted April 4, 2005.

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.

Present address: Fátima Al-Shahrour, Pablo Minguez, Juan M. Vaquerizas, Lucía Conde and Joaquín Dopazo, Bioinformatics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler 16, E46013, Valencia, Spain


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