Connecting extracellular metabolomic measurements to intracellular flux states in yeast

BMC Systems Biology

Table 1 Comparison of i MM904 and i LL672 gene deletion predictions and experimental data under minimal media conditions.

Media	Model	Method	True viable	False viable	False lethal	True lethal	True viable %	False viable %	MCC
*Glucose*	iMM904 full	FBA	647	10	32	33	95.29	23.26	0.60
	iMM904 full	linMOMA	644	10	35	33	94.85	23.26	0.58
	iMM904 full	MOMA	644	10	35	33	94.85	23.26	0.58
	iMM904 reduced	FBA	440	9	28	33	94.02	21.43	0.61
	iMM904 reduced	linMOMA	437	9	31	33	93.38	21.43	0.60
	iMM904 reduced	MOMA	437	9	31	33	93.38	21.43	0.60
	iLL672 full	MOMA	433	9	35	33	92.52	21.43	0.57
*Galactose*	iMM904 full	FBA	595	32	36	59	94.29	35.16	0.58
	iMM904 full	linMOMA	595	32	36	59	94.29	35.16	0.58
	iMM904 full	MOMA	595	32	36	59	94.29	35.16	0.58
	iMM904 reduced	FBA	409	12	33	56	92.53	17.65	0.67
	iMM904 reduced	linMOMA	409	12	33	56	92.53	17.65	0.67
	iMM904 reduced	MOMA	409	12	33	56	92.53	17.65	0.67
	iLL672 full	MOMA	411	19	31	49	92.99	27.94	0.61
*Glycerol*	iMM904 full	FBA	596	43	36	47	94.30	47.78	0.48
	iMM904 full	linMOMA	595	44	37	46	94.15	48.89	0.47
	iMM904 full	MOMA	598	44	34	46	94.62	48.89	0.48
	iMM904 reduced	FBA	410	20	34	46	92.34	30.30	0.57
	iMM904 reduced	linMOMA	409	21	35	45	92.12	31.82	0.56
	iMM904 reduced	MOMA	412	21	32	45	92.79	31.82	0.57
	iLL672 full	MOMA	406	20	38	46	91.44	30.30	0.55
*Ethanol*	iMM904 full	FBA	593	45	29	55	95.34	45.00	0.54
	iMM904 full	linMOMA	592	45	30	55	95.18	45.00	0.54
	iMM904 full	MOMA	592	44	30	56	95.18	44.00	0.55
	iMM904 reduced	FBA	408	21	27	54	93.79	28.00	0.64
	iMM904 reduced	linMOMA	407	21	28	54	93.56	28.00	0.63
	iMM904 reduced	MOMA	407	20	28	55	93.56	26.67	0.64
	iLL672 full	MOMA	401	13	34	62	92.18	17.33	0.68

MCC, Matthews correlation coefficient (see Methods). Note that the i LL672 predictions were obtained directly from [3] and thus the viability threshold was not optimized using the maximum MCC approach.

ISSN: 1752-0509