Absolute Enrichment: Gene Set Enrichment Analysis for Homeostatic Systems
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CitationSaxena, Vishal, Dennis Orgill, and Isaac Kohane. 2006. Absolute enrichment: gene set enrichment analysis for homeostatic systems. Nucleic Acids Research 34, no. 22: e151.
AbstractThe Gene Set Enrichment Analysis (GSEA) identifies sets of genes that are differentially regulated in one direction. Many homeostatic systems will include one limb that is upregulated in response to a downregulation of another limb and vice versa. Such patterns are poorly captured by the standard formulation of GSEA. We describe a technique to identify groups of genes (which sometimes can be pathways) that include both up- and down-regulated components. This approach lends insights into the feedback mechanisms that may operate, especially when integrated with protein interaction databases.
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