Deletion of cysR, the node having the highest connectivity among the regulators chosen from the regulatory network, resulted in a mutant which was insensitive to carolacton thus demonstrating not only the essentiality of cysR for the response of S. mutans biofilms to carolacton but also the relevance of the predicted network.
Different from other centrality measures, PeC determines a protein's essentiality not only based on its connectivity, but also whether it has a high probability to be co-clustered and co-expressed with its neighbors.
More importantly, the impact of extracellularity on mammalian protein evolutionary rate is not only independent from that of gene essentiality but also the greatest among all the factors examined.
As newsroom Latinos continue to decline, Nate is has been a notable exception in 2011 -- not only by keeping his job, but by increasing his essentiality to LATimes online.
Not only transcriptional abundance (codon adaptation index and expression level), but also protein-protein associations (PPAs), essentiality (ESS), subcellular localization of cytoplasmic membrane (SLM), transmembrane helices (TMH) and hydropathicity score (HS) independently and significantly affected the ERs of bacterial proteins.
By advanced techniques, based on the Lefschetz-type fixed point theorems and sophisticated degree arguments (fixed point index techniques), we are able to treat not only the sole existence problems, but also to guarantee certain sorts of a weak stability called nonejectivity and essentiality.
The revised tables (Supplementary Files 1-3) detail not only in/near which gene a particular mutation is located, but also its effect on the protein sequence (if any), the expression level of that gene in LB and minimal medium, essentiality status, COG functional class, and a number of properties relating to the difference between predicted WT and mutant RNA secondary structures.
Nevertheless, essentiality is not the only factor that could influence the presence of vertical signal in a set of genes.
This means that FBA can not predict essentiality with >44% precision, as can be seen on the precision-recall curve (Fig. 4).
However, current essential gene databases provide only binary essentiality data from genome-wide experiments (21, 22), and different fitness among genes has not been the focus of these databases.
