Method:

Over-representation - Fisher test comparison of a selected list of genes to a defined list of reference genes (i.e. genes on a chip). Test measures the probabilty that a random list would contain as many genes as the selected list in a given GeneSet. p-values are corrected for multiple testing using q-value correction.
Percent-coverage - Percent coverage is not a statistical test. It is used with presence - absence calls to identify the percent of a gene set category found in the selected list as compared to the reference list.

Enter a list of genes to analyze:

Paste a list of entrez gene IDs in this box to compare to the selected gene sets. Non-numerical characters are considered to be delimiters between gene ids. Multiple delimiters will be merged.

Choose from predefined Entrez ID gene lists:

A number of pre-defined reference gene lists are available for Affymetrix chips. The lists are created from the 'Entrez Gene' column from the annotation files provided by Affymetrix. Selecting '--- Input a custom gene list (Entrez IDs) ---' from the list will open a new text box into which a custom list of entrez gene ids can be pasted.

Available Predefined Gene Lists
Human Genome U133 Plus 2.0 Array	Gene IDs were extracted from the CSV formatted annotation file for this chip. Gene IDs were taken from the 'Entrez Gene' column. If a probeset with multiple gene mappings were omitted.
Human Genome U133A Array	Gene IDs were extracted from the CSV formatted annotation file for this chip. Gene IDs were taken from the 'Entrez Gene' column. Probesets with multiple gene mappings were omitted.
Mouse Genome 430 2.0 Array	Gene IDs were extracted from the CSV formatted annotation file for this chip. Gene IDs were taken from the 'Entrez Gene' column. Probesets with multiple gene mappings were omitted.
Mouse Genome 430A 2.0 Array	Gene IDs were extracted from the CSV formatted annotation file for this chip. Gene IDs were taken from the 'Entrez Gene' column. Probesets with multiple gene mappings were omitted.
Mouse Genome 430A Array	Gene IDs were extracted from the CSV formatted annotation file for this chip. Gene IDs were taken from the 'Entrez Gene' column. Probesets with multiple gene mappings were omitted.
Mouse Genome U74Av2 Array	Gene IDs were extracted from the CSV formatted annotation file for this chip. Gene IDs were taken from the 'Entrez Gene' column. Probesets with multiple gene mappings were omitted.

Enter the set of genes from which the above list was selected:

Optional input field which is only used if the predefined set is set to '--- Input a custom gene list (Entrez IDs) ---'. This option can be used with other reference lists created from other arrays or from other reference collections. (i.e. Genes in a cell-based screening library, etc.) Paste your customized reference list of entrez gene identifiers into this box. Any non-numerical character pasted into this box will be treated as a delimiter between IDs. Multiple consecutive delimiters will be treated as a single delimiter.

Source code for GeneSet Analyzer. This is a large file. (~80Mb)