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Bioinformatics Advance Access originally published online on October 10, 2006
Bioinformatics 2006 22(21):2643-2649; doi:10.1093/bioinformatics/btl450
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Survival analysis of longitudinal microarrays

Natasa Rajicic 1,2, Dianne M. Finkelstein 1,2,*, David A. Schoenfeld 1,2 and the Inflammation Host Response to Injury Research Program Investigators{dagger}

1 Massachusetts General Hospital, Biostatistics Unit 50 Staniford Street, Suite 560, Boston, MA, USA
2 Department of Biostatistics, Harvard School of Public Health Boston, MA, USA

*To whom correspondence should be addressed.

Motivation: The development of methods for linking gene expressions to various clinical and phenotypic characteristics is an active area of genomic research. Scientists hope that such analysis may, for example, describe relationships between gene function and clinical events such as death or recovery. Methods are available for relating gene expression to measurements that are categorized or continuous, but there is less work in relating expressions to an observed event time such as time to death, response or relapse. When gene expressions are measured over time, there are methods for differentiating temporal patterns. However, methods have not yet been proposed for the survival analysis of longitudinally collected microarrays.

Results: We describe an approach for the survival analysis of longitudinal gene expression data. We construct a measure of association between the time to an event and gene expressions collected over time. Statistical significance is addressed using permutations and control of the false discovery rate. Our proposed method is illustrated on a dataset from a multi-center research study of inflammation and response to injury that aims to uncover the biological reasons why patients can have dramatically different outcomes after suffering a traumatic injury (www.gluegrant.org).

Contact: dfinkelstein{at}partners.org

Received on May 11, 2006; revised on August 15, 2006; accepted on August 17, 2006

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