Figure 5

The distributions of GO term p-values and hierarchy levels for the DASSEM units, the transcription modules, and the random protein sets. The p-values of GO term enrichments for the DASSEM units (black), the transcription modules (gray), and the random sets of proteins (white) are shown in panel A. Since the range of p-values was large, the second logarithm, i.e. the logarithm of the absolute value of the first logarithm, was plotted for ease of visualization. The plot indicates that the number of GO terms and the values of the p-values were similar between the transcription modules and the DASSEM units. In contrast, there were much less terms associated with random sets of proteins, and the p-values of these terms were less significant. Panel B shows the levels of the GO terms within the GO hierarchy. For the transcription modules and the DASSEM units the depths of the GO term levels were similar. In contrast, the terms for the random protein sets were distributed at the higher GO levels where the terms are less specific.