Figure 1

Overview of AVID, using prediction of the molecular function of YOL137W as an example. Initially, YOL137W is treated as potentially functionally related to 6,448 other yeast proteins (not shown). Stage 2 prunes this to 30 putatively similar proteins, and the stage 3 decision tree further reduces this list to eight high-confidence neighbors. See additional file 2 for a description of the decision tree. In stage 4, five of the eight neighbors of YOL137W have existing AVID GO annotation (boxed) and "vote" to assign the GO term GO:0005355. After stage 4, proteins with known annotation in the figure are boxed, those with novel predictions are shown in diamonds and the function of YGR224W, in a hexagon, is a refined prediction. The estimated accuracy of predicted functional similarities (in stages 2 and 3) and annotations (in stage 4) are given in italics (see Methods). MF: molecular function; BP: biological process; CC: cellular component. Rosette figures generated using Graphviz [46].