Predicting Essential Genes and Proteins Based on Machine Learning and Network Topological Features: A Comprehensive Review

Genome-wide gene deletion studies have shown that a small fraction of genes in a genome are indispensable to the survival or reproduction of an organism (Winzeler et al., 1999; Kamath et al., 2003). These genes are referred as essential genes, and essential proteins are the products of essential genes. The deletion of such essential genes will result in lethality or infertility. Since being essential is highly dependent on the circumstances in which an organism lives, recently systematic attempts have been made to identify those genes that are absolutely required to maintain life, provided that all nutrients are available (Zhang and Lin, 2009). Such experiments have led to the conclusion that the absolutely required number of genes for a bacteria is on the order of about 250–300, which encode proteins to maintain a central metabolism, replicate DNA, translate genes into proteins, maintain a basic cellular structure, and mediate transport processes into and out of the cell.