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Updated: Jul 18, 2026

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
Published on: August 16, 2017
Absolute enrichment: gene set enrichment analysis for homeostatic systems
Vishal Saxena1, Dennis Orgill, Isaac Kohane
1Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. vishal@mit.edu
Abstract:
The 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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