Biological significance of predicted target gene sets using pathway analysis. Biological significance is shown with the help of the pathways enriched in the κB target gene sets predicted by the HMM at various thresholds. The y-axis shows the sum of the negative logarithm of the p-values of the top 25 enriched pathways. Gene sets predicted by the HMM are biologically significant as compared to randomly selected genes. They show a peak at the threshold occupancy probability of 0.5 (~800 genes). The thresholds used for obtaining the gene sets for the pathway analysis (occupancy probability threshold between 0.05 and 0.7) are indicated. HMM-predicted gene sets and randomly selected gene sets are indicated by blue and green curves, respectively. Only about 50–70% of the genes in each gene set are available for pathway analysis because the rest of the genes are not adequately annotated. The numbers in the figure, however, correspond to the number of genes in the entire gene sets.