Absolute enrichment: gene set enrichment analysis for homeostatic systems.
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.
Saxena
Vishal
V
Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. vishal@mit.edu
Orgill
Dennis
D
Kohane
Isaac
I
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