Figure 2.

Typical output from the GO-Stats program. From the input of a group of Drosophila genes, GO-stat returns a series of GO terms associated with them (columns 1 and 3). The terms are ranked according to a P-value representing their statistical relevance (column 8). The output also lists additional useful information: column 2 describes the depth at which a given GO term is found in the GO hierarchy (note that some terms can be found at several levels simultaneously; for example, GO:0009586). Columns 4 and 6 list the numbers of genes annotated for a given term in the reference and the user sets, respectively. Columns 5 and 7 list the corresponding occurrence frequencies. Finally, the last column indicates whether a given GO term is enriched (E) or depleted (D), based on the term frequency ratio (column 7/column 5). Note that hyperlinks to GO terms definitions by the GO consortium are provided (underlined in column 3). In such an output, all GO terms associated with the input genes are listed in the table. To visualize the hierarchy between these terms, an interactive functional feature is provided with GO-Stats: by clicking on a term (radio button on the left of GO terms list), all its parent terms in the list are highlighted. Finally, when working in the program, moving the mouse pointer on the GO ID column will make all the genes associated with a given GO term appear in a box.