Sorting the full genome by prediction of essentiality then manually evaluating secondary protein properties attempts to avoid the issues related to developing a nuanced automated system capable of filtering
down to a short list of candidate drug targets while still prioritizing the listing for high quality potential targets. MHS predicted a slightly smaller number of essential genes than experimentally found in the individual genome surveys comprising DEG. In contrast, GCS predicted a slightly larger set (Figure 6). Because most of the entries within DEG represent SHP099 in vitro genome wide surveys for essential genes we can compare the number of genes identified by our analysis to the number of essential genes in each DEG organism. Vibrio cholerae was removed as an outlier because it consists of 5 genes in DEG and does not represent a comprehensive genome survey. By MHS our analysis predicted approximately 250 genes or approximately 30% of the wBm genome as having reasonable confidence of essentiality. The raw number of predicted essential genes is lower than that for most of the DEG organisms, and under the mean for DEG of 392 genes. Mycoplasma genitalium and Mycoplasma pulmonis, which are also intracellular bacteria with genome sizes similar to wBm, have 381 and 310 genes within DEG, respectively. The relatively similar number of essential genes identified across DEG organisms suggests that these data are describing
a common set of genes across a shared set of important pathways. It appears that we are able to predict a quite significant portion of these in wBm through the MHS, though it does appear selleck products that MHS alone may not be identifying the complete set. By GCS we identified 544 wBm genes as important within Rickettsiales, comprising approximately Regorafenib 69% of the wBm genome. This is greater than the Mycoplasmas and most other DEG organisms, but still less than Haemophilus influenzae (642), M. tuberculosis (614),
or Escherichia coli (712) (Table 1). Overall, it appears that for prediction of essential genes both MHS and GCS score are effective. MHS is likely an incomplete survey. GCS prediction appears to identify a more complete set, encompassing all but 8 of the genes identified by MHS. However, the additional genes identified by GCS also probably include a number of genes that, while important, are not strictly essential. It is possible to overestimate the set of essential genes predicted by GCS as a result of using closely related organisms. PRIMA-1MET research buy Although we note that in the case of Rickettsiales, these organisms are in the process of reducing their genomes, adding significance to retained genes. Within the goals of this research, predicting essential genes as potential drug targets, our methods provide sufficient sensitivity and specificity as long as these caveats are recognized. Figure 6 Number of essential genes versus total number of Refseq genes. •-DEG organisms (V. cholerae omitted as an outlier). △-wBm essential gene prediction by MHS.