Supervised harvesting of expression trees

Trevor Hastie¹^,2, Robert Tibshirani²^,1 , David Botstein³ and Patrick Brown⁴

¹Department of Statistics, Stanford University, Stanford, CA 94305, USA

²Department of Health, Research & Policy, Stanford University, Stanford, CA 94305, USA

³Department of Genetics, Stanford University, Stanford, CA 94305, USA

⁴Department of Biochemistry, Stanford University, Stanford, CA 94305, USA

author email corresponding author email

Genome Biology 2001, 2:research0003.1-0003.12doi:10.1186/gb-2001-2-1-research0003


Published:	10 January 2001

Subject areas: Bioinformatics, Genome studies, Methods, Cancer, Medicine

Abstract

Background

We propose a new method for supervised learning from gene expression data. We call it 'tree harvesting'. This technique starts with a hierarchical clustering of genes, then models the outcome variable as a sum of the average expression profiles of chosen clusters and their products. It can be applied to many different kinds of outcome measures such as censored survival times, or a response falling in two or more classes (for example, cancer classes). The method can discover genes that have strong effects on their own, and genes that interact with other genes.

Results

We illustrate the method on data from a lymphoma study, and on a dataset containing samples from eight different cancers. It identified some potentially interesting gene clusters. In simulation studies we found that the procedure may require a large number of experimental samples to successfully discover interactions.

Conclusions

Tree harvesting is a potentially useful tool for exploration of gene expression data and identification of interesting clusters of genes worthy of further investigation.