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).