|Gene association rewriting examples|
|M1 Gene loss||R_0490||YJR051W||–|
|M2 Gene gain||R_2008||–||YALI0E34793g and YALI0D24431g|
|M3 Two othologs||R_0240||YPL104W||YALI0F26433g|
|M4 Duplication in scaffold ,||R_1413||YEL006W or YIL006W||YALI0E16478g|
|M5 Expansion in scaffold||R_0439||YIL009W or YMR246W or YOR317W||YALI0D17864g|
|M6 Duplication in target||R_1551||YBL064C and YCR083W||YALI0F08195g and (YALI0F01496g or YALI0E23540g)|
|M7 Expansion in target||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.
Loira et al.
Loira et al. BMC Systems Biology 2012 6:35 doi:10.1186/1752-0509-6-35