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Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates

André Fujita1*, Luciana Rodrigues Gomes2, João Ricardo Sato3, Rui Yamaguchi1, Carlos Eduardo Thomaz4, Mari Cleide Sogayar2 and Satoru Miyano1

Author Affiliations

1 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan

2 Chemistry Institute, University of São Paulo, Av. Lineu Prestes, 748, São Paulo-SP, 05508-900, Brazil

3 Mathematics, Computation and Cognition Center, Universidade Federal do ABC, Rua Santa Adélia, 166 – Santo André, 09210-170, Brazil

4 Department of Electrical Engineering, Centro Universitário da FEI, Av. Humberto de Alencar Castelo Branco, 3972 – São Bernardo do Campo, 09850-901, Brazil

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BMC Systems Biology 2008, 2:106  doi:10.1186/1752-0509-2-106

Published: 5 December 2008



Prostate cancer is a leading cause of death in the male population, therefore, a comprehensive study about the genes and the molecular networks involved in the tumoral prostate process becomes necessary. In order to understand the biological process behind potential biomarkers, we have analyzed a set of 57 cDNA microarrays containing ~25,000 genes.


Principal Component Analysis (PCA) combined with the Maximum-entropy Linear Discriminant Analysis (MLDA) were applied in order to identify genes with the most discriminative information between normal and tumoral prostatic tissues. Data analysis was carried out using three different approaches, namely: (i) differences in gene expression levels between normal and tumoral conditions from an univariate point of view; (ii) in a multivariate fashion using MLDA; and (iii) with a dependence network approach. Our results show that malignant transformation in the prostatic tissue is more related to functional connectivity changes in their dependence networks than to differential gene expression. The MYLK, KLK2, KLK3, HAN11, LTF, CSRP1 and TGM4 genes presented significant changes in their functional connectivity between normal and tumoral conditions and were also classified as the top seven most informative genes for the prostate cancer genesis process by our discriminant analysis. Moreover, among the identified genes we found classically known biomarkers and genes which are closely related to tumoral prostate, such as KLK3 and KLK2 and several other potential ones.


We have demonstrated that changes in functional connectivity may be implicit in the biological process which renders some genes more informative to discriminate between normal and tumoral conditions. Using the proposed method, namely, MLDA, in order to analyze the multivariate characteristic of genes, it was possible to capture the changes in dependence networks which are related to cell transformation.