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Feature selection environment for genomic applications

Fabrício Martins Lopes12*, David Corrêa Martins1* and Roberto M Cesar1

Author Affiliations

1 Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão 1010, 05508-090, São Paulo-SP, Brazil

2 COINF, Universidade Tecnológica Federal do Paraná, Av. Alberto Carazzai, 1640, 86300-000, Cornélio Procópio-PR, Brazil

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BMC Bioinformatics 2008, 9:451  doi:10.1186/1471-2105-9-451

Published: 22 October 2008

Abstract

Background

Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are many genomic and proteomic applications that rely on feature selection to answer questions such as selecting signature genes which are informative about some biological state, e.g., normal tissues and several types of cancer; or inferring a prediction network among elements such as genes, proteins and external stimuli. In these applications, a recurrent problem is the lack of samples to perform an adequate estimate of the joint probabilities between element states. A myriad of feature selection algorithms and criterion functions have been proposed, although it is difficult to point the best solution for each application.

Results

The intent of this work is to provide an open-source multiplataform graphical environment for bioinformatics problems, which supports many feature selection algorithms, criterion functions and graphic visualization tools such as scatterplots, parallel coordinates and graphs. A feature selection approach for growing genetic networks from seed genes (targets or predictors) is also implemented in the system.

Conclusion

The proposed feature selection environment allows data analysis using several algorithms, criterion functions and graphic visualization tools. Our experiments have shown the software effectiveness in two distinct types of biological problems. Besides, the environment can be used in different pattern recognition applications, although the main concern regards bioinformatics tasks.