Table 2

Gene association rewriting examples
Case Reaction Scaffold Target
M1 Gene loss <a onClick="popup('http://www.biomedcentral.com/1752-0509/6/35/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1752-0509/6/35/mathml/M1">View MathML</a> R_0490 YJR051W
M2 Gene gain <a onClick="popup('http://www.biomedcentral.com/1752-0509/6/35/mathml/M2','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1752-0509/6/35/mathml/M2">View MathML</a> R_2008 YALI0E34793g and YALI0D24431g
M3 Two othologs <a onClick="popup('http://www.biomedcentral.com/1752-0509/6/35/mathml/M3','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1752-0509/6/35/mathml/M3">View MathML</a> R_0240 YPL104W YALI0F26433g
M4 Duplication in scaffold <a onClick="popup('http://www.biomedcentral.com/1752-0509/6/35/mathml/M4','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1752-0509/6/35/mathml/M4">View MathML</a>, <a onClick="popup('http://www.biomedcentral.com/1752-0509/6/35/mathml/M5','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1752-0509/6/35/mathml/M5">View MathML</a> R_1413 YEL006W or YIL006W YALI0E16478g
M5 Expansion in scaffold <a onClick="popup('http://www.biomedcentral.com/1752-0509/6/35/mathml/M6','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1752-0509/6/35/mathml/M6">View MathML</a> R_0439 YIL009W or YMR246W or YOR317W YALI0D17864g
M6 Duplication in target <a onClick="popup('http://www.biomedcentral.com/1752-0509/6/35/mathml/M7','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1752-0509/6/35/mathml/M7">View MathML</a> R_1551 YBL064C and YCR083W YALI0F08195g and (YALI0F01496g or YALI0E23540g)
M7 Expansion in target <a onClick="popup('http://www.biomedcentral.com/1752-0509/6/35/mathml/M8','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1752-0509/6/35/mathml/M8">View MathML</a> 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

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