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Advances in Bioinformatics
Volume 2008, Article ID 789026, 7 pages
http://dx.doi.org/10.1155/2008/789026
Research Article

NCR-PCOPGene: An Exploratory Tool for Analysis of Sample-Classes Effect on Gene-Expression Relationships

Departament de Bioquímica i Biología Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain

Received 14 February 2008; Revised 23 April 2008; Accepted 17 October 2008

Academic Editor: Pierre Rouzé

Copyright © 2008 Juan Cedano et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background. Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data. Our tools allow researchers to test and formulate from a hypothesis to entire models. Results. The objective of the NCRPCOPGene is to study the relationships among gene expressions under different conditions, to classify these conditions, and to study their effect on the different relationships. The web application makes it easier to define the sample classes, grouping the microarray experiments either by using (a) biological, statistical, or any other previous knowledge or (b) their effect on the expression relationship maintained among specific genes of interest. By means of the type (a) class definition, the researcher can add biological information to the gene-expression relationships. The type (b) class definition allows for linking genes correlated neither linearly nor nonlinearly. Conclusions. The PCOPGene tools are especially suitable for microarrays with large sample series. This application helps to identify cellular states and the genes involved in it in a flexible way. The application takes advantage of the ability of our system to relate gene expressions; even when these relationships are noncontinuous and cannot be found using linear or nonlinear analytical methods.