EASE: Annotation Over-representation Analysis
Advanced Parameter Information
Directory Selection for Support Files
Custom EASE FileSystem
This option enables the selection of a local directory to be used as the source for annotation
files for EASE analysis. Multiple file systems can be present to support a variety of array
types. Selection of a file system directs file choosers to that area, however, file selections
may be made outside of selected base file system if appropriate. Note that the selected directory
should be the directory that contains the "Data" directory. In MeV's default data dircetory this
would be the 'ease' directory.
Population Selection
The population selection panel allows the user to specify whether the
population set of gene indices should be loaded from a file or if the population set should be
taken as all indices loaded in the current Multiple Experiment Viewer. Note that if the current
viewer does not contain all population indices it is important to use the default option of a
population file.
A population file is a list of indices representing the indices from which the cluster
was segregated by statistical or other means. The file format consists of a column of indices with
one index per line. The population often represents a set of indices representing each element
on the array, however, there are circumstances where one might wish to disregard particular
spots such as internal controls.
MeV Annotation Key
This area contains a drop down list which contains a list of available annotation types which can be
used identify genes. Generally it's best to use an index or accession which 'uniquely' identifies
the spotted material.
Annotation Conversion File
This optional file provides the mapping from your annotation key (above) to the index used to map to
biological themes (GO terms, KEGG pathways, etc.). If your annotation key type is the one used in the
linking file (below) then this conversion (mapping) is not needed.
Gene Annotation / Gene Ontology Linking Files
This section allows one to specify one or more annotation files. These files contain gene indices
paired with biological themes such as go terms.
File Selection Scenario
One possible example of the file linking structure could be:
[GenBank#]-->[GenBank#]:[locus_link_id]-->[locus_link_id]:[go_term]
This shows the progression from 'Annotation Key', to conversion file (converting GenBank# to locus_link_id),
to final linking with GO terms. Keep in mind that although shown with a single arrow, in general
one gene index will map to many GO terms (or other biological theme or pathway categories).