Among these models, the simplest one is prediction of essential genes based on the known essentiality of homologous genes [ 18- 21].
Based on the different essentiality of metabolites, the metabolites were classified into three groups: Universal Metabolites (UM): Some inorganic or cofactor metabolites, such as CMP and ATP, which have been found to exist universally in more than 90% organisms.
One of the important heuristics based on the concept of essentiality ratio for maximization of throughput and minimization of system unbalance simultaneously was proposed by [Mukhopadhyay et al. (1992)].
Though a simple interpretation for the P E - t correlation is that the capability of duplicate compensation decays with the evolutionary time since the duplication [ 11], some other alternatives cannot be ruled out, which were based on the correlation of gene essentiality with, for instance, sequence conservation or protein connectivity [ 9, 10, 24].
Based on the hypothesis that essential genes are persistent during the long evolutionary process, we recently developed a new prediction tool (Geptop) that offers gene essentiality annotations for bacterial genomes (8) (http://cefg.uestc.edu.cn/geptop/).uestc.edu.cn/geptop/
We also consider a more traditional graph measure for the essentiality of signaling components based on the number of all simple paths (SPs) from inputs to outputs: where NSP G and NSP G Δvv) denote the total number of simple paths from the input(s) to the output(s) in the original expanded network G and the damaged network G Δv after deleting v, respectively.
The former is randomly or systematically used to inactivate potential essential genes, and gene essentiality could be determined based on the living situation of the organism.
Moreover, another explanation of the exceptions they found for Buchnera can be attributed to authors' assignment of gene essentiality, which was exclusively based on the homology with E. coli.
The next field provided a filter based on the following: Name/Annotation, Features, Structures, Expression, Antigenicity, Phylogenetic distribution, Essentiality, Validation data, Druggability, Assayability, and Bibliographic references.
Essentiality of human genes was evaluated based on the data on mouse lethal phenotypes, which were retrieved from the Mouse Genome Informatics database ([ 89], www.informatics.jax.org).org
