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From genes to functional classes in the study of biological systems

Fátima Al-Shahrour1, Leonardo Arbiza1, Hernán Dopazo1, Jaime Huerta-Cepas12, Pablo Mínguez1, David Montaner12 and Joaquín Dopazo12*

Author Affiliations

1 Bioinformatics Department, Autopista del Saler 16, E46013, Valencia, Spain

2 Functional Genomics Node, INB-CIPF Centro de Investigación Príncipe Felipe (CIPF), Autopista del Saler 16, E46013, Valencia, Spain

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BMC Bioinformatics 2007, 8:114  doi:10.1186/1471-2105-8-114

Published: 3 April 2007

Abstract

Background

With the popularisation of high-throughput techniques, the need for procedures that help in the biological interpretation of results has increased enormously. Recently, new procedures inspired in systems biology criteria have started to be developed.

Results

Here we present FatiScan, a web-based program which implements a threshold-independent test for the functional interpretation of large-scale experiments that does not depend on the pre-selection of genes based on the multiple application of independent tests to each gene. The test implemented aims to directly test the behaviour of blocks of functionally related genes, instead of focusing on single genes. In addition, the test does not depend on the type of the data used for obtaining significance values, and consequently different types of biologically informative terms (gene ontology, pathways, functional motifs, transcription factor binding sites or regulatory sites from CisRed) can be applied to different classes of genome-scale studies. We exemplify its application in microarray gene expression, evolution and interactomics.

Conclusion

Methods for gene set enrichment which, in addition, are independent from the original data and experimental design constitute a promising alternative for the functional profiling of genome-scale experiments. A web server that performs the test described and other similar ones can be found at: http://www.babelomics.org webcite.