A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

BMC Systems Biology

Table 2 Gene association rewriting examples

Case	Reaction	Scaffold	Target
M1 Gene loss $S_{1} \to Ø$	R_0490	YJR051W	–
M2 Gene gain $Ø \to T_{1}$	R_2008	–	YALI0E34793g and YALI0D24431g
M3 Two othologs $S_{1} \to T_{1}$	R_0240	YPL104W	YALI0F26433g
M4 Duplication in scaffold $S_{1} \to T_{1}$ , $S_{2} \to T_{1}$	R_1413	YEL006W or YIL006W	YALI0E16478g
M5 Expansion in scaffold $S_{1 k N} \to T_{1}$	R_0439	YIL009W or YMR246W or YOR317W	YALI0D17864g
M6 Duplication in target $S_{1} \to (T_{1} o r T_{2})$	R_1551	YBL064C and YCR083W	YALI0F08195g and (YALI0F01496g or YALI0E23540g)
M7 Expansion in target $S_{1} \to (T_{1} o r T_{2} o r K T_{N})$	R_0415	YGL205W and YIL160C and YKR009C	YALI0E15378g and YALI0E18568g and (YALI0E27654g or YALI0F10857g or YALI0C23859g or YALI0E32835g or YALI0E06567g or YALI0D24750g)

Associations of genes to reactions in the model are useful for redundancy, and necessary for simulation of knockouts. When these associations are inherited from the scaffold, they must be rewritten to take into account expansion and contraction of protein families defined for homologous genes. The following examples illustrate the seven cases treated by the method.

ISSN: 1752-0509