Selecting informative genes for discriminant analysis using multigene expression profiles.
BACKGROUND
Gene expression data extracted from microarray experiments have been used to study the difference between mRNA abundance of genes under different conditions. In one of such experiments, thousands of genes are measured simultaneously, which provides a high-dimensional feature space for discriminating between different sample classes. However, most of these dimensions are not informative about the between-class difference, and add noises to the discriminant analysis.


RESULTS
In this paper we propose and study feature selection methods that evaluate the "informativeness" of a set of genes. Two measures of information based on multigene expression profiles are considered for a backward information-driven screening approach for selecting important gene features. By considering multigene expression profiles, we are able to utilize interaction information among these genes. Using a breast cancer data, we illustrate our methods and compare them to the performance of existing methods.


CONCLUSIONS
We illustrate in this paper that methods considering gene-gene interactions have better classification power in gene expression analysis. In our results, we identify important genes with relative large p-values from single gene tests. This indicates that these are genes with weak marginal information but strong interaction information, which will be overlooked by strategies that only examine individual genes.
Yan
Xin
X
Russell Investments, Tacoma, WA, USA. XYan@russell.com
Zheng
Tian
T
D000465:Algorithms; D014408:Biomarkers, Tumor / Q000235:genetics; D001943:Breast Neoplasms / Q000235:genetics; D016002:Discriminant Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods
D014408:Biomarkers, Tumor