Figure 2

Validation of GO term selection by sensitivity and specificity. We show in (a) that the sensitivity and specificity of our GO term selection mechanism declines as we enforce a stricter definition of a true positive GO term selection. We show the sensitivity and specificity for each of the three biological domains: molecular function (MF), biological process (BP) and cellular component (CC). In (b) and (c) we show the changes in sensitivity and specificity when searching short and long motifs respectively. We attribute the increase in sensitivity and decrease in specificity for short motifs to the naturally larger number of records in a sequence database matched by a shorter motif, leading to fewer false negatives and more false positives. Values for these charts can be found in additional file 1, and detailed node selection reports used to generate this chart can be found in additional files 2, 3 and 4.