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Figure
.
.
Reconstruction of a genetic network based on the fitting of the top-scoring triplets to Xu's
model, where A
−+
(
−−
) B denotes that A activates (represses) B, respectively
rithm is a pioneer application of the response surface method that is used to recon-
struct genetic networks. Unfortunately, it failed to reconstruct the TC interactions of
interest. his stimulated Shieh and her colleagues to develop a regression approach,
as described below.
Although the SRSapproach utilizes the principlethat an activator activates its tar-
get gene's expression and a repressor represses its target gene's expression, the coe
-
cients of the response surface in Equation (
.
) were based only on that the effect of
A (R) is positive (negative) and the resulting expression level of the target gene falls
in the interval
(personal communication with Xu). In fact, there are an infinite
number of sets of coe
cients that satisfy the boundary condition. In biology, genes
with similar functions may have similar interaction patterns. Similar patterns of in-
teractionstendtoidentifycomponentsfromthesamebiologicalpathway(Tongetal.,
). herefore, it was proposed that the surface should be determined by the data,
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