Bioinformatics and Biology Insights

Using a Seed-Network to Query Multiple Large-Scale Gene Expression Datasets from the Developing Retina in Order to Identify and Prioritize Experimental Targets

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Bioinformatics and Biology Insights 2008:2 401-412

Published on 01 Feb 2008

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Laura A. Hecker1, Timothy C. Alcon2, Vasant G. Honavar3 and M. Heather West Greenlee4

1Interdepartmental Neuroscience Program, Iowa State University, Ames, IA 50011. 2Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA 50011. 3Department of Computer Science, Bioinformatics and Computational Biology Graduate Program, Center for Computational Intelligence, Learning and Discovery, Iowa State University, Ames, IA 50011. 4Department of Biomedical Sciences, Interdepartmental Neuroscience Program, Bioinformatics and Computational Biology Graduate Program, Center for Computational Intelligence, Learning and Discovery, Iowa State University, Ames, IA 50011.


Understanding the gene networks that orchestrate the differentiation of retinal progenitors into photoreceptors in the developing retina is important not only due to its therapeutic applications in treating retinal degeneration but also because the developing retina provides an excellent model for studying CNS development. Although several studies have profiled changes in gene expression during normal retinal development, these studies offer at best only a starting point for functional studies focused on a smaller subset of genes. The large number of genes profiled at comparatively few time points makes it extremely difficult to reliably infer gene networks from a gene expression dataset. We describe a novel approach to identify and prioritize from multiple gene expression datasets, a small subset of the genes that are likely to be good candidates for further experimental investigation. We report progress on addressing this problem using a novel approach to querying multiple large-scale expression datasets using a ‘seed network’ consisting of a small set of genes that are implicated by published studies in rod photoreceptor differentiation. We use the seed network to identify and sort a list of genes whose expression levels are highly correlated with those of multiple seed network genes in at least two of the five gene expression datasets. The fact that several of the genes in this list have been demonstrated, through experimental studies reported in the literature, to be important in rod photoreceptor function provides support for the utility of this approach in prioritizing experimental targets for further experimental investigation. Based on Gene Ontology and KEGG pathway annotations for the list of genes obtained in the context of other information available in the literature, we identified seven genes or groups of genes for possible inclusion in the gene network involved in differentiation of retinal progenitor cells into rod photoreceptors. Our approach to querying multiple gene expression datasets using a seed network constructed from known interactions between specific genes of interest provides a promising strategy for focusing hypothesis-driven experiments using largescale ‘omics’ data.




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