A Time Matching System Based on Microarray Gene Expression ...

tripastroturfΤεχνίτη Νοημοσύνη και Ρομποτική

7 Νοε 2013 (πριν από 3 χρόνια και 11 μήνες)

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Genomewide analysis of Dynamical genetic network of
Escherichia coli

Wong Yung
-
Hao(
翁永豪

Y慮朠䍨g
-
䑵D朠g
楊冀冬
)
,

Hsi
-
Yuan Huang

(
黃熙淵
)


College of Biological Science and Technology, NCTU



The
E.coli
genome contains more than 4000 genes that are classified into

16
modules of different functions. They form a complicated genetic network, there exists
a lot of models to simulate this network. Such as Boolean networks, Bayesian
networks, graph theory , qualitative models , stochastic models and rule
-
based
formalisms
.

There are several important modules in the network, such as CRP
activation module, DNA supercoiling module and input or output module related to
the outside stimuli.

The dynamical behavior in this network is very important. We try
to reveal the universal

properties in the
E.coli

genetic network and apply to other
species. We’ll explore the multiple steady
-
states, periodic, chaotic and other nonlinear
dynamical system behaviors of
E.coli

We will concern about the TF and mRNA
relationship
s

, and the reactio
ns about transcription, translation and PTMs.

We use
coupling differential equations to describe this dynamical systems, analyze it with
quantitative and qualitative simulations. And then use the tools such as AUTO,
PHASER, Oscill8 and GNA to run the compl
ex dynamical behavior in
E.coli
.
PHASER provides a numerical simulations of differential and difference equations,
we use it to simulate the general behavior of the network. AUTO is a bifurcation
analyzer, we use it to do the nonlinear analysis of the regu
latory network. Oscill8 is a
tool for analyzing large systems of ODEs, especially on the high dimensional
parameter space, when the network becomes large, we use this tool to analyze. GNA
is based on the piecewise differential equation theory, when we nee
d to do qualitative
analysis

Key word:
genetic network,
E.coli,

bifurcation, GNA