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Bioinformatics Advance Access originally published online on September 27, 2006
Bioinformatics 2006 22(23):2890-2897; doi:10.1093/bioinformatics/btl492
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A scalable method for integration and functional analysis of multiple microarray datasets

Curtis Huttenhower , Matt Hibbs , Chad Myers and Olga G. Troyanskaya *

Department of Computer Science, Lewis-Sigler Institute for Integrative Genomics, Princeton University Princeton, NJ, USA

*To whom correspondence should be addressed.

Motivation: The diverse microarray datasets that have become available over the past several years represent a rich opportunity and challenge for biological data mining. Many supervised and unsupervised methods have been developed for the analysis of individual microarray datasets. However, integrated analysis of multiple datasets can provide a broader insight into genetic regulation of specific biological pathways under a variety of conditions.

Results: To aid in the analysis of such large compendia of microarray experiments, we present Microarray Experiment Functional Integration Technology (MEFIT), a scalable Bayesian framework for predicting functional relationships from integrated microarray datasets. Furthermore, MEFIT predicts these functional relationships within the context of specific biological processes. All results are provided in the context of one or more specific biological functions, which can be provided by a biologist or drawn automatically from catalogs such as the Gene Ontology (GO). Using MEFIT, we integrated 40 Saccharomyces cerevisiae microarray datasets spanning 712 unique conditions. In tests based on 110 biological functions drawn from the GO biological process ontology, MEFIT provided a 5% or greater performance increase for 54 functions, with a 5% or more decrease in performance in only two functions.

Contact: ogt{at}cs.princeton.edu

Supplementary information: Supplementary data, a collection of predictions made by MEFIT and software implementing MEFIT are available online at http://function.princeton.edu/mefit/.

Received on July 31, 2006; revised on September 5, 2006; accepted on September 19, 2006

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