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Activity Number: 131
Type: Contributed
Date/Time: Monday, July 30, 2012 : 8:30 AM to 10:20 AM
Sponsor: Biometrics Section
Abstract - #306654
Title: Principal Variable-Based Gene Selection for Expression Assay
Author(s): Jie Ding*+ and Giovanni Parmigiani
Companies: Dana-Farber Cancer Institute and Harvard School of Public Health
Address: 10 Peabody Terrace Apt 21, Cambridge, MA, 02138, United States
Keywords: Gene expression ; Gene selection
Abstract:

Although whole-genome gene expression essays are readily available nowadays, under certain situations it is still desirable to measure only a subset of genes, often with higher accuracy and reliability or in a tissue-specific design. We are investigating the problem of selecting a near-optimal subset of genes based on existing gene expression data in the absence of phenotypic information for the design of later assays. The goal is to identify a group of genes that best represent the variation of all the measured genes. This is analogous to the principal component analysis, with the key difference being that the subset here consists of individual genes instead of linear combinations of genes. We base our method on the idea of principal variables and take two different computational approaches: a general stochastic search algorithm and a fast stepwise algorithm. We apply both algorithms to simulated data and several cancer genome data sets. The resulting subsets of genes are evaluated for their abilities to predict expression levels of genes outside the subsets as well as phenotypes in the data. Our method is also applicable to other similar large-scale feature selection problems.


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