Methods Update for Liao et al. (2006) Mol Biol Evol 23: 2072-2080

A bug in the authors' computer program caused a number of errors during the compilation of the lists of mouse essential genes and nonessential genes. This bug has been fixed and all the analyses have been repeated based on an updated mouse genome annotation (Ensembl v38 and MGI 3.51). In the reanalysis, we used the same definition for gene essentiality as before. That is, mouse genes with targeted deletion phenotype of embryonic lethality (MP: 0002080), prenatal lethality (MP: 0002081), post-natal lethality (MP: 0002082), premature death or induced morbidity (MP: 0002083), abnormal reproductive system morphology (MP: 0002160) or abnormal reproductive system physiology (MP: 0001919) were grouped as essential genes. All other genes associated with a phenotypic annotation, including those entries with a normal phenotype, were grouped as nonessential genes. As a result, the dataset included 1,642 mouse essential genes and 1,341 mouse nonessential genes that have rat orthologs. Genes used for partial correlation analyses were limited to autosomal genes with expression data. Thus, the updated Table 1 and Table 2 are based on 1,255 essential and 959 nonessential genes. All other aspects of the methods remain unchanged from our original methods.