Figure 10

Variability of functional similarity in the E. coli genome. Functional similarity (Y-axis) here is an all-by-all category GO score or funSim average among the genes included in the local window. The X-axis is the genome position of the left-hand side of the window. The red line indicates the threshold value of functional similarity we used for individual analysis of a genome window for overrepresentation of GO terms (0.7 for each category GO score average, 0.49 for funSim average). The dots denote known clusters of functionally similar genes. For the BP graph, neon green is the lac operon, pink is the trp operon, and dark blue is the his operon. For the MF graph, dark red dots are ATP synthase components (atpX). And for the CC graph, dark green dots are proteins of the ribosome. The same plots for yeast and malaria genomes are not provided since they have much larger genomes (yeast and malaria have 16 and 14 chromosomes, respectively) but all the data are available on our website.