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In-Depth Information
set of the PSO cost function. Checked against RT-PCRs, the prediction accuracy of
eSEM ranges from
% to
%. Overall, the prediction accuracies of eSEM when
appliedtothealphadata setinSpellmanetal.(
)wereashighas
%(about
%
onaverage).Figures
.
and
.
motivated the incorporation ofthe areas enclosed by
the RT curves versus those enclosed by the AT curves into eSEM, which improved
the aforementioned prediction accuracy to
% for the alpha data set. his example
demonstrates how visualization aids the development of methodology.
Acknowledgement.
heauthorswishtothankDrs.Chung-MingChenandMing-YenCheng
forconstructivediscussions.hisresearchwassupportedinpartbytheNationalScienceCoun-
cil grant
-
-M
-
and Academia Sinica Biotechnology development grant
-
to
G.S.S.
References
Aburatani, S., Saito, S., Toh, S. and Horimoto, K. (
) A graphical chain model
for inferring regulatory systems network from gene expression profiles. Statistical
Methedology,
:
-
.
Akutsua, T., Kuhava, S., Maruyamac, O. and Miyano, S. (
). Identification of ge-
netic networks by strategic gene disruptions and gene overexpressions under a
Boolean model. heoretical Computer Science,
:
-
.
Arkin, A.P. and Ross, J. (
). Statistical construction of chemical-reaction mecha-
nisms from measured time-series. J. Phys. Chem,
:
-
.
Arkin, A.P., Shen, P.D. and Ross, J. (
).A Test Case of A Correlation Metric Con-
struction of A Reaction Pathway from Measurements. Science,
:
-
.
Bar-Joseph, Z., Gerber, G., Gifford, D.K., Jaakkola, T.S. and Simon, I. (
). A new
approach to analyzing gene expression time series data. In Myer, G., Hannen-
halli,S.,Sankoff,D.,Istrail,S.,Pevzner,P.andWaterman,M.(eds)Proceedings
of the
th annual international conference on Computational Biology.ACM,New
York, pp.
-
.
Barabási, A.-L. and Oltvai, Z.N. (
). Network Biology: Understanding the cell's
functional organization. Nature Reviews,
:
-
.
Beal, M.J.,Falciani, F.,Ghahramani, Z., Rangel, C. and Wild,D.L.(
).ABayesian
approach to reconstructing genetic regulatory networks with hidden factors.
Bioinformatics,
:
-
.
Cho, R.J., Campbell, H.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L.,
Wolfsberg, T.G., Gabrielian, A.E., Lansman, D., Lockhart, D.J. and Davis, R.W.
(
).A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular
Cell,
:
-
.
Chuang, C.L., Chen, C.M. and Shieh, G.S. (
). A pattern recognition approach to
infer genetic networks. Technical Report C
-
, Institute of Statistical Science,
Academia Sinica, Taiwan.
Dillon, W.R. and Goldstein, M. (
). Multivariate analysis. Wiley, New York.
De Jong, H.(
).Modeling and Simulation of Genetic Regulatory Systems: a liter-
ature review. Journal of Computational Biology,
:
-
.
