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Open Access Database

PathEx: a novel multi factors based datasets selector web tool

Eric Bareke1*, Michael Pierre1, Anthoula Gaigneaux1, Bertrand De Meulder1, Sophie Depiereux1, Naji Habra2 and Eric Depiereux1*

Author Affiliations

1 Molecular Biology Research Unit (URBM), University of Namur - FUNDP, Namur, Belgium

2 Research Center in Information Systems Engineering (PReCISE), University of Namur - FUNDP, Namur, Belgium

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BMC Bioinformatics 2010, 11:528  doi:10.1186/1471-2105-11-528

Published: 22 October 2010

Abstract

Background

Microarray experiments have become very popular in life science research. However, if such experiments are only considered independently, the possibilities for analysis and interpretation of many life science phenomena are reduced. The accumulation of publicly available data provides biomedical researchers with a valuable opportunity to either discover new phenomena or improve the interpretation and validation of other phenomena that partially understood or well known. This can only be achieved by intelligently exploiting this rich mine of information.

Description

Considering that technologies like microarrays remain prohibitively expensive for researchers with limited means to order their own experimental chips, it would be beneficial to re-use previously published microarray data. For certain researchers interested in finding gene groups (requiring many replicates), there is a great need for tools to help them to select appropriate datasets for analysis. These tools may be effective, if and only if, they are able to re-use previously deposited experiments or to create new experiments not initially envisioned by the depositors. However, the generation of new experiments requires that all published microarray data be completely annotated, which is not currently the case. Thus, we propose the PathEx approach.

Conclusion

This paper presents PathEx, a human-focused web solution built around a two-component system: one database component, enriched with relevant biological information (expression array, omics data, literature) from different sources, and another component comprising sophisticated web interfaces that allow users to perform complex dataset building queries on the contents integrated into the PathEx database.