Fig. 3

Results pages containing iTerms enriched in the input gene list. In this case the list was sorted by p-values as determined by Fisher’s exact test. One can use the Frequency text box to eliminate iTerms that have fewer genes associated with them based on the user’s cutoff. The Selection buttons allow one to “Select All”, Clear the selections or Toggle selected iTerms. Also, individual iTerms can be selected by clicking. The selection features are used to remove irrelevant iTerms based on the users knowledge. One can include blacklisted iTerms (see text) by selecting the check box. The Reset Table button can be used to recreate the starting table should errors be made while deleting iTerms thought to be irrelevant. The Concept Map View and Cytoscape View open new windows with the corresponding representations of the iTerm:gene pairs. Hovering over an iTerm box will display the genes associated with that iTerm from the input list along with the p-value of that iTerm