Evaluating correlation coefficients for clustering gene expression profiles of cancer

Pablo A. Jaskowiak*, Ricardo J.G.B. Campello, Ivan G. Costa


Publikation: Kapitel i bog/rapport/konference-proceedingKonferencebidrag i proceedingsForskningpeer review


Cluster analysis is usually the first step adopted to unveil information from gene expression data. One of its common applications is the clustering of cancer samples, associated with the detection of previously unknown cancer subtypes. Although guidelines have been established concerning the choice of appropriate clustering algorithms, little attention has been given to the subject of proximity measures. Whereas the Pearson correlation coefficient appears as the de facto proximity measure in this scenario, no comprehensive study analyzing other correlation coefficients as alternatives to it has been conducted. Considering such facts, we evaluated five correlation coefficients (along with Euclidean distance) regarding the clustering of cancer samples. Our evaluation was conducted on 35 publicly available datasets covering both (i) intrinsic separation ability and (ii) clustering predictive ability of the correlation coefficients. Our results support that correlation coefficients rarely considered in the gene expression literature may provide competitive results to more generally employed ones. Finally, we show that a recently introduced measure arises as a promising alternative to the commonly employed Pearson, providing competitive and even superior results to it.

TitelAdvances in Bioinformatics and Computational Biology - 7th Brazilian Symposium on Bioinformatics, BSB 2012, Proceedings
ISBN (Trykt)9783642319266
StatusUdgivet - 2012
Udgivet eksterntJa
Begivenhed7th Brazilian Symposium on Bioinformatics, BSB 2012 - Campo Grande, Brasilien
Varighed: 15. aug. 201217. aug. 2012


Konference7th Brazilian Symposium on Bioinformatics, BSB 2012
ByCampo Grande
SponsorConselho Nacional Desenvolvimento Cientifico Tecnologico (CNPq), Coordenacao de Aperfeicoamento Pessoal de Nivel Superior (CAPES), Fund. Apoio Desenvolv. Ensino, Cienc. Tecnol.Estado, Mato Grosso do Sul (Fundect), Fundacao de Apoio a Pesquisa ao Ensino e a Cultura (FAPEC)
NavnLecture Notes in Computer Science
Vol/bind7409 LNBI


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