EASE: Annotation Over-representation Analysis

Parameter Information


Support Directory /Annotation Parameter Selection

Select EASE File System

This button allows the download of EASE annotation file systems for a selected species and clone set. A selection dialog will allow species selection from a variety of plant and animal species. A list of many commercially available arrays for the selected species is also presented for selection.

Custom

This button enables the user to specify different sources for annotation directories, population selection, annotation conversion files and gene ontology linking files.

Mode Selection

Cluster Analysis

This mode performs annotation analysis on a selected subset (sample list or cluster) of the full data set loaded in MeV. The output is a list of biological 'themes' represented in the cluster and a statistic reporting the probability that a particular theme is over represented in the cluster relative to it's representation in the entire data set. The resulting table will initially be sorted by this statistic.

Annotation Survey

The survey mode simply produces a list of biological themes that are represented in the data currently loaded in the viewer from which Ease is launched. Note that this could be a subset of the total slide data. If you want to survey all annotation on the slide you have to use a viewer with all of the slide's data loaded. The initial ordering of the output table is based on the prevalence of a theme in the data set (hit count). This mode can be used to cluster genes based on biological themes. The clusters can then be stored and marked (colored) for tracking during cluster analysis.

Cluster Selection

This section permits selection of a cluster for analysis. The default population set of genes is composed of all indices loaded in the current Multiple Experiment Viewer. To define the population to which clusters should be compared against, please refer to the "Advanced" option above.

The cluster panel displays gene clusters currently stored in MeV's cluster repository. If no clusters have been saved then a blank browser page or empty table will be displayed and the Cluster Analysis mode option will be disabled. Selecting a row in the cluster table will display the cluster in the expression graph area of the browser. EASE cluster analysis will operate on the selected cluster.

Statistical Parameter Selection

Nested EASE

This button allows the use of Nested EASE. The Nested EASE algorithm executes after the EASE run is complete, executing a second, sub-level, iterative Fisher's Exact Test on significantly enriched GO terms identified in a first-level EASE analysis.

Advanced

This button permits specification of reported statistical and trimming parameters.