Finding gene clusters for a replicated time course study

BMC Research Notes

Steven G Self¹  Linda Breeden²  Li-Xuan Qin³ 

[1] Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA

关键词: Time course;    Replications;    Regression;    Microarray;    Clustering;   

Others  :  1134726
DOI  :  10.1186/1756-0500-7-60

 received in 2013-07-25, accepted in 2014-01-15,  发布年份 2014

【 摘 要 】

Background

Finding genes that share similar expression patterns across samples is an important question that is frequently asked in high-throughput microarray studies. Traditional clustering algorithms such as K-means clustering and hierarchical clustering base gene clustering directly on the observed measurements and do not take into account the specific experimental design under which the microarray data were collected. A new model-based clustering method, the clustering of regression models method, takes into account the specific design of the microarray study and bases the clustering on how genes are related to sample covariates. It can find useful gene clusters for studies from complicated study designs such as replicated time course studies.

Findings

In this paper, we applied the clustering of regression models method to data from a time course study of yeast on two genotypes, wild type and YOX1 mutant, each with two technical replicates, and compared the clustering results with K-means clustering. We identified gene clusters that have similar expression patterns in wild type yeast, two of which were missed by K-means clustering. We further identified gene clusters whose expression patterns were changed in YOX1 mutant yeast compared to wild type yeast.

Conclusions

The clustering of regression models method can be a valuable tool for identifying genes that are coordinately transcribed by a common mechanism.

【 授权许可】

   
2014 Qin et al.; licensee BioMed Central Ltd.

【 图 表 】

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