using evolutionary conserved modules in gene networks as a strategy to leverage high throughput gene expression queries使用进化保守基因网络的模块作为策略利用高通量基因表达查询.pdfVIP

Using Evolutionary Conserved Modules in Gene Networks as a Strategy to Leverage High Throughput Gene Expression Queries 1 2 3,4 Jeanne M. Serb *, Megan C. Orr , M. Heather West Greenlee 1 Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa, United States of America, 2 Department of Statistics, Iowa State University, Ames, Iowa, United States of America, 3 Bioinformatics and Computational Biology Program, Department of Biomedical Sciences, Iowa State University, Ames, Iowa, United States of America, 4 Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America Abstract Background: Large-scale gene expression studies have not yielded the expected insight into genetic networks that control complex processes. These anticipated discoveries have been limited not by technology, but by a lack of effective strategies to investigate the data in a manageable and meaningful way. Previous work suggests that using a pre-determined seed- network of gene relationships to query large-scale expression datasets is an effective way to generate candidate genes for further study and network expansion or enrichment. Based on the evolutionary conservation of gene relationships, we test the hypothesis that a seed network derived from studies of retinal cell determination in the fly, Drosophila melanogaster, will be an effective way to identify novel candidate genes for their role in mouse retinal development. Methodology/Principal Findings: Our results demonstrate that a number of gene relationships regulating retinal cell differentiation in the fly are identifiable as pairwise correlations between genes from developing mouse retina. In addition, we demonstrate that our extracted seed-network of corr