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.