How to identify essential genes from molecular networks?

BMC Systems Biology

Table 3 Comparison of statistical parameters used to estimate the efficacy to identify essential metabolic genes in yeast

Model	Method	Essentials/Non-essentials	Sensitivity	Specificity	Error	Accuracy	Reference
iFF708	FBA	23/90	0.13	1	0.87	82%	22
iFF708	FBA	91/508	0.31	0.95	0.69	85%	6
iFF708	FBA	79-146/562-629	0.40-0.53	90-96%	NR	NR	33
iND750	FBA	118/NR	0.31	NR	NR	NR	10
iLL672	FBA	NR/NR	0.68-0.80	96-98%	NR	NR	33
iFF708	MOMA	46/302	0.60	0.92	0.41	88%	34
iLL672	MOMA	NR/NR	0.73-0.80%	NR	NR	NR	33
iND750	SA	100/NR	0.14	NR	NR	NR	7

Previous studies on the efficiency to identify essential metabolic genes on yeast, report different statistical parameters of confidence (Sensitivity, Specificity, Error and Accuracy columns), and commonly use a single network (Model column) and a single method (Method column) to identify essential genes. The data were obtained from the works reported in the "Reference" column. FBA: Flux-Balance Analysis; MOMA: Method of Minimization of Metabolic Adjustment; SA: Synthetic accessibility; NR: a value not reported in the cited reference.

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