Improving identification of differentially expressed genes in microarray studies using information from public databases |
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Authors: | Richard D Kim Peter J Park |
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Affiliation: | (1) Harvard-Partners Center for Genetics and Genomics, 77 Avenue Louis Pasteur, 02115 Boston, MA, USA;(2) Children's Hospital Informatics Program, 300 Longwood Ave, 02115 Boston, MA, USA; |
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Abstract: | We demonstrate that the process of identifying differentially expressed genes in microarray studies with small sample sizes can be substantially improved by extracting information from a large number of datasets accumulated in public databases. The improvement comes from more reliable estimates of gene-specific variances based on other datasets. For a two-group comparison with two arrays in each group, for example, the result of our method was comparable to that of a t-test analysis with five samples in each group or to that of a regularized t-test analysis with three samples in each group. Our results are further improved by weighting the results of our approach with the regularized t-test results in a hybrid method. |
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