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Table 8.2. Couples are classified by rows as 'essential' (ES) or 'not essential' (NES) if
experimental data proof the yeast survival or death, and by column if they have topological
'alternatives' (A) or not (MA) to arcs deletions. These alternatives can be: other pathways (P),
multiple genes synthesizing the same enzymatic function (G) or supplementary enzymes involved
in the reaction (E).
A
MA
ES
TDH2 (YJR009C) - TDH3 (YGR192C) (E,G)
ADE16 (YLR028C) - ADE17 (YMR120C)
ARO3 (YDR035W) - ARO4 (YBR249C)
PGM1 (YKL127W) - PGM2 (YMR105C)
URA5 (YML106W) - URA10 (YMR271C)
LYS20 (YDL182W) - LYS21 (YDL131W)
GSY1 (YFR015C) - GSY2 (YLR258W)
SER3 (YER081W) - SER33 (YIL074C)
TKL1 (YPR074C) - TKL2 (YBR117C)
ASN1 (YPR145W) - ASN2 (YGR124W)
NES
DAL7 (YIR031C) - MLS1 (YNL117W) (G,P)
ADH1 (YOL086C) - ADH2 (YMR303C) (G)
GDH1 (YOR375C) - GDH3 (YAL062W) (E)
GLT1 (YDL171C) - GDH3 (YAL062W) (E)
GLT1 (YDL171C) - GDH1 (YOR375C) (E)
TDH1 (YJL052W) - TDH2 (YJR009C) (E,G)
TDH1 (YJL052W) - TDH3 (YGR192C) (E,G)
MIS1 (YBR084W) - SHM1 (YBR263W) (E,G)
FUR1 (YHR128W) - URA5 (YML106W)
ALD2 (YMR170C) - ALD3 (YMR169C)
APT1 (YML022W) - APT2 (YDR441C)
AAH1 (YNL141W) - APT2 (YDR441C)
SHM1 (YBR263W) - SHM2 (YLR058C)
SHM1 (YBR263W) - GCV1 (YDR019C)
GCV1 (YDR019C) - SHM2 (YLR058C)
In some cases predictions of double essentiality deduced by the Segrè group
do not agree with both the topological analysis and the experimental data. As an
example, FBA predicts yeast survival after the deletion of both URA5 and
URA10, while both the graph analysis and De Montigny experimental study say
the opposite.
The same considerations apply when two more couples have been taken into
account: SER3-SER33 (isozymes, whose essentiality is found from Albers), and
LYS20-LYS21, whose lethality estimated by Segrè is 0.96 (thus considered non
essential), but whose essentiality is experimentally proved by Feller and
colleagues. This result demonstrates a slight superiority of our very simple
method with respect to the most sophisticated FBA in predicting the biological
consequences of double mutations.
Looking at Table 8.2 and focussing on the main effects of inhibitions of
essential enzymes listed before, one can argue the existence of a close
relationship between essentiality/non essentiality and the presence of topological
connections. The causes and evolution of gene dispensability has remained a
controversial issue. It is also intuitive that the existence of many alternatives is
synonymous of dispensability and robustness: duplicated genes as well as more
