Sensitivity Analysis and Experimental Design

- case study of an NF-kB signal pathway

Hong Yue
Manchester Interdisciplinary Biocentre (MIB)
The University of Manchester
h.yue@manchester.ac.uk
Colloquium on Control in Systems Biology, University of Sheffield, 26
th
March, 2007
NF-kB signal pathway
Time-dependant local sensitivity analysis
Global sensitivity analysis
Robust experimental design
Conclusions and future work



Outline
NF-kB signal pathway
Hoffmann et al., Science, 298, 2002
| |
| |
0 0
1 2
1 2
( , , ), ( )
(state vector)
(parameter vector)
= =
=
=
T
n
T
m
X f X t X t X
X x x x
k k k
u
u
stiff nonlinear ODE model
0 0.5 1 1.5 2 2.5
x 10
4
0
0.01
0.02
0.03
0.04
0.05
0.06
0.07
0.08
0.09
time/s

N
F
-
k
B
n

(
x
1
5
)



















Nelson et al., Sicence, 306, 2004
State-space model of NF-kB
states definition
Characteristics of NF-kB signal pathway
Important features:
Oscillations of NF-kB in the nucleus
delayed negative feedback regulation by IkBo
Total NF-kB concentration
2 3 5 7 9 12 14 15 17 19 21
0 x x x x x x x x x x x + + + + + + + + + + =
14
61 10
8
i
i
x k x
=
=

Total IKK concentration

Control factors:
Initial condition of NF-kB
Initial condition of IKK
Determine how sensitive a system is with respect to the
change of parameters
Metabolic control analysis
Identify key parameters that have more impacts on the
system variables
Applications: parameter estimation, model discrimination &
reduction, uncertainty analysis, experimental design
Classification: global and local
dynamic and static
deterministic and stochastic
time domain and frequency domain
About sensitivity analysis
0 0
0
0
( , , ), ( )
, ( )
j j j j j
j j
X f X t X t X
f X f
S J S F S t S
X
u
u u
= =

c c c

= + = + =

c c c

Time-dependent sensitivities (local)

Direct difference method (DDM)
0
, , 0
/ , ( ) ( ) =c c =
i j i j i j j i
s x s t x u o u
Sensitivity coefficients
Scaled (relative) sensitivity coefficients
,
/
/
j
i i i
i j
j j j i
x x x
s
x
u
u u u
c c
= =
c c
Sensitivity index
2
, ,
1
1
( )
N
i j i j
k
RS s k
N
=
=

Local sensitivity rankings
Sensitivities with oscillatory output
Limit cycle oscillations:
Non-convergent sensitivities
Damped oscillations:
convergent sensitivities
Dynamic sensitivities
Correlation
analysis
Identifiability
analysis
Robust/fragility
analysis
Parameter estimation framework
based on sensitivities
Yue et al., Molecular BioSystems, 2, 2006
Model
reduction
Parameter
estimation
Experimental
design
Sensitivities and LS estimation
Assumption on measurement noise:
additive, uncorrelated and normally distributed with zero
mean and constant variance.
Gradient
,
( , )
( ) ) ( ( )
i
i i i i
k i k i
j
i
j
j
x k J
g k r s r k k
u
e e
u u
c c
= = =
c c

Least squares criterion for parameter estimation
( )
2
1
2
( ) ( ) ( , )
i i i
k i
J x k x k u e u =

2
,
,
,
( )
( , ) ( ( ) ( ) )
i i j i l
k i
j
i j
i
k
l
i
i
l
J
H j l s k s
s
r k
k
k e e
u u u
c
c
= =
c c

c

Hessian matrix
Correlation matrix
( )
c
M correlation S =
Understanding correlations
cost functions w.r.t. (k
28
, k
36
) and (k
9
, k
28
).
Sensitivity coefficients for NF-kB
n
.
K
28
and k
36
are correlated
Global sensitivity analysis: Morris method
One-factor-at-a-time (OAT) screening method
Global design: covers the entire space over which the
factors may vary
Based on elementary effect (EE). Through a pre-defined
sampling strategy, a number (r) of EEs are gained for each
factor.
Two sensitivity measures: (mean), (standard deviation)

Max D. Morris, Dept. of Statistics, Iowa State University
large : high overall influence
(irrelevant input)

large : input is involved with
other inputs or whose effect is
nonlinear
sensitivity ranking - plane
Sensitive parameters of NF-kB model

k28, k29, k36, k38
k52, k61
k9, k62 k19, k42
Global sensitive Local sensitive
k29: IkBo mRNA degradation
k36: constituitive IkBo translation
k28: IkBo inducible mRNA synthesis
k38: IkBo
n
nuclear import
k52: IKKIkBo-NF-kB association
k61: IKK signal onset slow adaptation
k9: IKKIkBo-NF-kB
catalytic
k62: IKKIkBo catalyst
k19: NF-kB nuclear
import
k42: constitutive IkB|
translation
IKK, NF-kB, IkBo
Improved data fitting via estimation
of sensitive parameters

(a) Hoffmann et al., Science (2002)
(b) Jin, Yue et al., ACC2007
The fitting result of NF-kB
n
in the IkBo-NF-kB model
Optimal experimental design

Basic measure of optimality:
Aim: maximise the identification information while minimizing the
number of experiments
What to design?
Initial state values: x
0
Which states to observe: C
Input/excitation signal: u(k)
Sampling time/rate
Fisher Information Matrix
1 T
FIM S Q S

=
Cramer-Rao theory
2 1

i
FIM
u
o

>
lower bound for the variance of unbiased
identifiable parameters
A-optimal
D-optimal
E-optimal
Modified E-optimal design
Optimal experimental design

maxdet( ) FIM
min
max ( ) FIM
1
min trace( ) FIM

Commonly used design principles:
min cond( ) FIM
u
1
u
2
1.96 , 1.96
i i
i i
u u
u o u o
(
+

95% confidence interval
The smaller the joint confidence intervals are, the
more information is contained in the measurements
Measurement set selection

Estimated parameters:
19 29 31 36
38 42 52 61
, , , ,
, , ,
k k k k
k k k k
x
12
(IKKIkB|-NF-kB), x
21
(IkBc
n
-NF-kB
n
), x
13
(IKKIkBc) , x
19
(IkB|
n
- NF-kB
n
)
Forward selection with modified E-optimal design
Step input amplitude
95% confidence intervals when :-
IKK=0.01M (r) modified E-optimal
design
IKK=0.06M (b) E-optimal design
Robust experimental design

Aim: design the experiment which should valid for a range of
parameter values
1
1 1
, ,
, 1, 0,
, ,
m
m
i i
i m
x x
i e e
e e
=

= = >
`
)

0
1
( , )
(nominal)
m
T T
i
i i i i
i
f x
FIM
=
c
= =
c

u
u
evv v
u
( )
1
1
(with uncertainty)
( , , )
m
T
i i i i
i
m
FIM
blkdiag
=
= A
A A s

e vv

This gives a (convex) semi-definite programming problem for

which there are many standard solvers (Flaherty, Jordan,
Arkin, 2006)
Measurement set selection
Robust experimental design

C
o
n
t
r
i
b
u
t
i
o
n

o
f

m
e
a
s
u
r
e
m
e
n
t

s
t
a
t
e
s

Uncertainty degree
max
0 (optimal design) (uniformdesign)
( ) (robust design) middle
=

Importance of sensitivity analysis

Benefits of optimal/robust experimental design
Conclusions
Future work
Nonlinear dynamic analysis of limit-cycle
oscillation
Sensitivity analysis of oscillatory systems
Acknowledgement
Dr. Martin Brown, Mr. Fei He, Prof. Hong Wang (Control Systems
Centre)
Dr. Niklas Ludtke, Dr. Joshua Knowles, Dr. Steve Wilkinson, Prof.
Douglas B. Kell (Manchester Interdisciplinary Biocentre, MIB)
Prof. David S. Broomhead, Dr. Yunjiao Wang (School of
Mathematics)
Ms. Yisu Jin (Central South University, China)
Mr. Jianfang Jia (Chinese Academy of Sciences)
BBSRC project Constrained optimization of
metabolic and signalling pathway models:
towards an understanding of the language
of cells