What is GSEA?

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

MeV has supported the Gaggle framework since September 2008 (MeV v4.2). Gaggle is a powerful communications system that allows connects supported programs (geese) to seamlessly transmit data to one another, without the need for intermediate flat files. MeV can use the Gaggle to send and receive data with other systems biology platforms, such as R, Cytoscape, and various web databases.

MultiExperiment ViewerMeV is a desktop application for the analysis, visualization and data-mining of large-scale genomic data. It is a versatile microarray tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery. Thousands of biologists have downloaded and used MeV to examine their data with an easy-to-use, graphical interface.

Nested EASE (nEASE) is an extension of EASE. The nEASE algorithm includes a second, sub-level, iterative Fisher’s Exact Test on significantly enriched GO terms identified in a first-level EASE analysis. This sub-classification approach provides increased sensitivity for detecting enriched GO terms and thus affords a deeper understanding of possible mechanisms underlying a given condition under study. nEASE was added to MeV as a new feature for version 4.5.