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Clustering gene expression profile data by selective shrinkage

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  • Ishwaran, Hemant
  • Sunil Rao, J.

Abstract

Clustering of gene expression profiles is a widely used approach for finding macroscopic data structure. A complication in such analyses is that not all genes are informative for forming clusters and different clusters might have different transcription regulation. Driven by these considerations, we present a novel two-stage clustering approach. The first stage identifies informative genes by adaptive variable selection using pseudo-samples modeled by a high dimensional multigroup ANOVA model. Variables are selected using a rescaled spike and slab Bayesian hierarchical model having a special selective shrinkage property. The second stage uses output from the first stage for clustering. We demonstrate why selective shrinkage occurs, and by extension, why it is useful for the clustering paradigm. We analyze a human gene atlas expression dataset where the question of interest is to look for tissue-specific transcription regulation and investigate whether tissues can be grouped together due to similar genomic control.

Suggested Citation

  • Ishwaran, Hemant & Sunil Rao, J., 2008. "Clustering gene expression profile data by selective shrinkage," Statistics & Probability Letters, Elsevier, vol. 78(12), pages 1490-1497, September.
    • Handle: RePEc:eee:stapro:v:78:y:2008:i:12:p:1490-1497
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    References listed on IDEAS

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    1. Ishwaran H. & Rao J.S., 2003. "Detecting Differentially Expressed Genes in Microarrays Using Bayesian Model Selection," Journal of the American Statistical Association, American Statistical Association, vol. 98, pages 438-455, January.
    2. Ishwaran, Hemant & Rao, J. Sunil, 2005. "Spike and Slab Gene Selection for Multigroup Microarray Data," Journal of the American Statistical Association, American Statistical Association, vol. 100, pages 764-780, September.
    3. Efron B. & Tibshirani R. & Storey J.D. & Tusher V., 2001. "Empirical Bayes Analysis of a Microarray Experiment," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 1151-1160, December.
    4. John D. Storey, 2002. "A direct approach to false discovery rates," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(3), pages 479-498, August.
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    1. Asafu-Adjei Josephine & Tadesse Mahlet G. & Coull Brent & Balasubramanian Raji & Lev Michael & Schwamm Lee & Betensky Rebecca, 2017. "Bayesian Variable Selection Methods for Matched Case-Control Studies," The International Journal of Biostatistics, De Gruyter, vol. 13(1), pages 1-23, May.

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