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Open Access Software

ProbFAST: Probabilistic Functional Analysis System Tool

Israel T Silva12*, Ricardo ZN Vêncio1, Thiago YK Oliveira12, Greice A Molfetta12 and Wilson A Silva12

Author Affiliations

1 Department of Genetics, Faculty of Medicine, University of São Paulo, Ribeirão Preto, Brazil

2 National Institute of Science and Technology in Stem Cell and Cell Therapy, Center for Cell Therapy and Regional Blood Center, Ribeirão Preto, Brazil

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BMC Bioinformatics 2010, 11:161  doi:10.1186/1471-2105-11-161

Published: 30 March 2010

Abstract

Background

The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis.

Results

We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes.

Conclusions

ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast webcite.