title: Absolute enrichment: gene set enrichment analysis for homeostatic systems.
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.
authors.affiliation: Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. vishal@mit.edu
authors.forename: Vishal
authors.initials: V
authors.lastname: Saxena
authors.forename: Dennis
authors.initials: D
authors.lastname: Orgill
authors.forename: Isaac
authors.initials: I
authors.lastname: Kohane
mesh_terms: D000465:Algorithms; D015536:Down-Regulation; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006706:Homeostasis; D006801:Humans; D007889:Leiomyoma / Q000235:genetics / Q000378:metabolism; D015854:Up-Regulation; D014594:Uterine Neoplasms / Q000235:genetics / Q000378:metabolism