GONOME scoring function: S (X, T ). Genomic positions in the input set X are shown with arrows. Regions belonging to genes annotated with GO term T are shaded red. Regions belonging to other genes are shaded green. Transcribed regions are shown in solid color. Upstream (downstream) regions are shown with horizontal (vertical) crosshatching. Unscored regions are shown as horizontal black lines. Positions in green and unscored regions receive association score of zero. Other positions receive association scores equal to the appropriate region weight. Panel A illustrates the simplest case where upstream and downstream regions of adjacent genes do not overlap. In panel B, the position x2 lies in the "overlap" region of two "red" genes, so its score is the sum of the upstream and downstream weights.