Boolean Modeling and Simulation of Tumor

Necrosis Factor- Signaling Network

Satyajit Rao
27th June 2013

Abstract
Tumor necrosis factor- is known for its anti tumor effects. Molecular details of TNF- signaling pathway have been elucidated well. However,
mechanism of regulation between two opposing decisions, survival and death,
remains unclear. Understanding of this mechanism could lead to identification of target molecules in order to favour apoptosis, and eventually to an
improvement in treatment. Using Boolean modeling, we try to compute dynamic steady states as a tool to predict a cells response to TNF- ligation.
We analyse the steady states in a systematic manner, with the ultimate aim
of determining an optimal set of target nodes in the above stated interest.

Contents

List of Tables

iv

List of Figures

1 Introduction

2 Basins of Attraction for Random Networks

2.1

Response to stimuli . . . . . . . . . . . . . . . . . . . . . . . .

2.2

Dynamic Network Model . . . . . . . . . . . . . . . . . . . . .

2.3

Dynamic Equations . . . . . . . . . . . . . . . . . . . . . . . .

2.4

Attractors and basin of attraction . . . . . . . . . . . . . . . .

2.5

Numerical simulations . . . . . . . . . . . . . . . . . . . . . .

2.6

Simulation results . . . . . . . . . . . . . . . . . . . . . . . . .

3 Boolean Modeling and Simulation

11

3.1

Boolean formalism for qualitative modeling . . . . . . . . . . . 12

3.2

Structural Analysis . . . . . . . . . . . . . . . . . . . . . . . . 13

3.3

Dynamic Analysis . . . . . . . . . . . . . . . . . . . . . . . . . 14

3.4

Network Reduction . . . . . . . . . . . . . . . . . . . . . . . . 15

3.5

Simulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

3.6

Initialization . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
3.6.1

3.7

Housekeeping Constraint . . . . . . . . . . . . . . . . . 16

Simulations in MATLAB . . . . . . . . . . . . . . . . . . . . . 16

4 Methods of Quantitative Analysis of Attractors

18

4.1

Analysis of Distance . . . . . . . . . . . . . . . . . . . . . . . 18

4.2

Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

4.3

Stability Analysis . . . . . . . . . . . . . . . . . . . . . . . . . 20
4.3.1

Steady State Stability . . . . . . . . . . . . . . . . . . 20

4.3.2

Asynchronous Markovian perturbation . . . . . . . . . 21

5 Case Study Results

23

5.1

Modeling TNF- Network . . . . . . . . . . . . . . . . . . . . 23

5.2

Distance Analysis . . . . . . . . . . . . . . . . . . . . . . . . . 25
5.2.1

min-Hamming Distance

. . . . . . . . . . . . . . . . . 25

5.3

Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

5.4

Stability Analysis . . . . . . . . . . . . . . . . . . . . . . . . . 26
5.4.1

Perturbation analysis for steady states . . . . . . . . . 26

5.4.2

Asychronous Markovian perturbation for cyclic attractors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

5.5

Phenotype switch . . . . . . . . . . . . . . . . . . . . . . . . . 29

5.6

Toll-Like Receptor (TLR) Network . . . . . . . . . . . . . . . 30

6 Conclusions and future work

32

Bibliography

33
ii

Bibliography

34

Appendices

37

A A simulation example: TOYNET

38

B Identifying unsteady part of network

40

C TNF pathway

43

D List of Interactions

44

iii

List of Tables
5.1

Sets of nodes randomized or constrained while initializing . . . 24

5.2

Truth table for phenotype based classification of steady states

26

D.1 Table of Interactions in TNF- signaling . . . . . . . . . . . . 44

D.2 Index of Species Alias used in Table D.1 . . . . . . . . . . . . 53

iv

List of Figures
2.1

Random network: distribution of size of basin of attraction . .

2.2

Basin of attraction distribution for Storkey & Valabregue rule

10

5.1

Flowchart for constructing Signaling Networks . . . . . . . . . 24

5.2

Distribution of Hamming distances for a set of attractors . . . 25

5.3

Histograms for transition fractions in TNF steady state stability analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

5.4

distribution of transition fractions returning to the same state

for asynchronous perturbations . . . . . . . . . . . . . . . . . 29

5.5

Transition fractions for TLR network . . . . . . . . . . . . . . 31

A.1 Interaction hypergraph of a sample network TOYNET . . . . 39

B.1 frequency with which a particular node is changing states in
a set of cycles . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
B.2 Part of TNF network responsible for unsteady behaviour . . . 42
C.1 Figure shows a part of TNF- signaling network in CellDesigner 43

Chapter 1
Introduction
Interactions among biomolecules are being studied and elucidated at a very
fast pace. Complex networks of interactions involving both intracellular and
extracellular biomolecules (signaling networks) emerging out of these studies, give us clues as to how a cell reacts to environmental stimuli. Tools for
studying biological functions and reaction mechanisms of these biomolecules
are very well established. It is the integrated behaviour of these networks as
a whole, however, that has not been studied to a large extent.

Leaving the study of individual biological entities, a paradigm of study

of biological systems as a whole, has emerged as the field of Systems Biology. This field uses Mathematical and Computational modeling techniques to
attempt to extract biological understanding from an integrated systems perspective. The modeling formalism used is usually correlated with the amount
of data one has about the system. Various formalisms exist, one extreme being Ordinary Differential Equation paradigm, which is a true representation

of interactions in a chemical reaction format. This is one extreme since it requires a huge amount of kinetic data to completely model one network. The
other extreme is to compute graphical representations for networks, which
is a data-driven regression approach as opposed to the specificity of ODEs.[11]

Modeling of networks in a logic-based way is an approach lying between

the two extremes, in that it requires minimal data about the reaction kinetics, yet it can be used to study dynamics and make predictions on the
networks behaviour. First used by Kauffman [8] to model gene regulation
process, this modeling technique has garnered a lot of interest, since it came
to light that certain dynamic steady states from logic-based model might
correspond to specific cell phenotypes.[7]

TNF- is a multifunctional cytokine playing a key role in apoptosis as

well as cell survival in addition to inflammation and immunity. Antitumor
activity of TNF- was shown in 1975 when William Coley found Coleys
toxin, whose active component was isolated as TNF-, caused haemorrhagic
necrosis of mice tumors [13]. It is known to exert cytotoxicity towards some
cell lines in vitro while causing hemorrhagic tumor necrosis in vivo without
affecting normal cells [14]. Though the complete underlying mechanism is
unknown, the potential selective antitumoral activity has created interest
in the cytokine. Currently TNF- is used synergistically with chemotherapy drugs in regional treatment of locally advanced soft tissue sarcomas and
metastatic melanomas to avoid limb amputation [19].

In this project, we curate, model and simulate a Boolean network of Tumor Necrosis Factor - signaling. The aim of the project is to find a set of
most likely targets which can switch a cells fate from survival to apoptosis
upon ligation by TNF-. From the simulations, we find steady states and
limit cycles and conduct quantitative analysis of their stability. We also qualitatively classify the steady states based on the two end responses of TNF-
signaling: apoptosis and survival, using biological markers. We conduct a
similar modeling and simulation exercise on another signaling network (Tolllike receptor, TLR) and perform the same stability analysis.

Chapter 2 contains a graph theoretical exercise which deals with modeling and simulating undirected random networks. We create attractors using
some learning rules, and then study their stability to random stimuli (perturbations) using dynamic network models. Chapter 3 discusses the formalism
of Boolean modeling and provides details of the simulation procedure.

Chapter 4 describes methods of quantitative analysis of attractors found

using synchronous simulation procedure. Chapter 5 presents the results obtained by simulating real networks, TNF- and TLR.

Chapter 2
Basins of Attraction for
Random Networks
2.1

Response to stimuli

It is important for a network to respond with high sensitivity for small but
important stimuli as well as with robustness to large stimuli. Scale free
topologies that are often found in nature, are seen to enable high sensitivity
to directed stimuli yet protecting the network from failure to random stimuli.
Lot of recent studies have gone into studying topology of network formed by
links (connections) between nodes. The distribution of these links, the degree
distribution, carries important information about the networks capacity. [2]

2.2

Dynamic Network Model

We use the Little-Hopfield model [10],[6]. This assumes that each node is
influenced by the states of other nodes to which it is linked. Such models are
useful to study the properties of multiple network states as attractors of the
dynamics [2]. An undirected graph with N labelled nodes n edges distributed
such that degree distribution is exponential or scale free, is the system. Each
node has two internal Ising spin states of i = 1 [4] The topology of the
network is stored in a network adjacency matrix I with element Iij = 1 if i and
j are nearest neighbours else zero [20]. The influence of nearest neighbours
depends on the patterns stored. In general we can store any number of
patterns using Hebbian learning rule of neural networks
p

1 X

Jij = Iij
p =1 i j

2.3

(2.1)

Dynamic Equations

Local field is defined at each vertex i by

hi (t) =

Jij j (t)

(2.2)

Where j (t) is the spin state at time t at vertex j. So the field is a weighted
sum of all spins states of nearest neighbouring nodes, the weights (Jij ) being
determined by the p stored patterns. Parallel dynamics are used in which,

at time t, all spins are updated synchronously using Glauber dynamics as[5],



1

+1 with probability 1 + exp 2hi (t)

T0
i (t + t) =
1



1 with probability 1 + exp 2hi (t)

T0

(2.3)

We use the local majority rules for time evolution of spin patterns, which is
actually Glauber dynamics at zero temperature. Thus,

i (t + 1) =

+1 if hi (t) > 0

(2.4)

1 if hi (t) < 0
If however, hi (t) = 0 we select the spin of that state to be +1 or -1 with
equal probability. [20]

2.4

Attractors and basin of attraction

A subset of state space to which orbits originating from typical initial conditions tend as time increases is called an attractor. For an attractor, the set
of initial conditions with long time behaviour approaching the attractor is
called its basin of attraction. An attractor can be identified with a functional
state of the system.[2]

Impact of external stimuli can be understood through response of a system to perturbation as a measure of robustness for the process of switching
between attractors. Since this is an undirected network, an edge between i
and j is not different from an edge between j and i. hence it can be deduced
6

that the influence matrix J is symmetric.

A particular state of a network is a collection of spins of all the N nodes.

A pattern is a state which is a functional state (and so an attractor of the
dynamics) to be learnt by a network. For the current simulation, two random
states are chosen from the state space and are learnt as patterns. This learning sets the pairwise influence between nodes Jij such that they are stable
states of the network.

For sufficiently large number of links and for a broad range of network
topologies, this form of non-zero pairwise influence will make the randomly
selected patterns into attractors [2]. Now that the attractors are set, we
can confirm that these are attractors by measuring size of their basin of
attraction. A stimulus is modelled by flipping certain number of nodes of
the pre-selected patterns and the resulting state is used as initial state for
the dynamical equations. Size of basin of attraction for a given attractor
is that number of nodes that need to be flipped before the dynamics of the
network fails to bring it back to the attractor state.

2.5

Numerical simulations

A 200 node random network with connection probability of 0.04 was created.
The expected number of nodes n is 796. 1000 simulations were carried out
for random stimuli (flipping random nodes). The number of nodes flipped
was increased until the dynamics failed to bring it back to original state.
7

Simulation procedure:
1. Generate a random network adjacency matrix was generated with parameters N=200, p=0.04
2. Generate two random state vectors out of the state space to store as
patterns in the adjacency matrix
3. Proceed to make them attractors by the Hebbian imprinting rule
4. Flip n nodes to get an initial state for dynamical equations, update
spins using dynamical equations.
5. If the state doesnt come back to the attractor, that n is the size of basin
of attraction. If it does come back, increase n and repeat procedure

2.6

Simulation results

Figure 2.1: histogram obtained for a 1000 simulations of a 200 node network
with connection probability 0.04. B is the size of basin of attraction (in
number of nodes)

A histogram for size of basin of attraction in 1000 simulations was obtained.

The histogram is approximately centred around 100, this shows that basin of
attraction for a random network to a random stimulus is 50% of the nodes.

The same algorithm was employed, but with a different learning rule-

Storkey and Valabregue [17] given by:

Jij0 = 0i, j and Jij = Jij1 +

1 1
1
i j i hji hij j
n
n
n

(2.5)

where
hij

n
X

1
Jik
k

(2.6)

k=1,k6=i,j

The distribution of sizes of basin of attraction for this rule is shown in 2.2

Figure 2.2: Basin of attraction distribution for Storkey & Valabregue rule

10

Chapter 3
Boolean Modeling and
Simulation
With the increase in data available about biological interactions due to advances in technology, disciplines like Systems Biology have emerged. Such
disciplines try to model and analyze the immense amount of data using mathematical modeling techniques. Gene regulation, metabolism, signal transduction are being studied at a high rate giving rise to the need for coherent
representation of whole systems.[15] Modeling complex interactions of a large
number of proteins is intuitively represented by a network. Interactions in a
network are represented by directed edges, pointing in the direction of mass
(flux) transfer or signal propagation. Species in the network are represented
by nodes. Further, an edge can have a sign along with a direction, with
positive sign modeling activation and negative, inhibition.[15]

11

3.1

Boolean formalism for qualitative modeling

A set of biological interactions is represented by a network. For further analysis however, the graph must be converted into a set of equations, i.e. a
model. A signal transduction network can be modeled either in a discrete
or a continuous space. Continuous models include ODEs for the different
reactions while discrete models include Boolean models and Petri Nets [16].
A qualitative modeling formalism represents each entity by a variable which
can only take up a finite set of values. However, the set of values may not
be linearly correlated with the actual concentrations of the entity.

The continuous ODE model requires a large amount of kinetic data which
is rarely available. Hence Boolean models introduced by S. Kauffman [8] and
R. Thomas [18] are preferred since they require no parameters. Each node
can have two distinct states: ON (1) and OFF (0) when their concentration
levels are above and below respective thresholds.

Boolean equations are constructed with the following rules:

The AND condition models the situation where two or more species are
simultaneously required to be at high concentrations for the reaction
to occur.

St+1 (1) = St (5) AND St (6)

12

 The OR conditions model situations where any one species at high concentration is enough for the reaction to occur.

St+1 (2) = St (3) OR St (4)

NOT condition models the inhibition of one species by another.

St+1 (3) = NOT St (7)

Thus, modeling signal transduction interactions as a network provides

a unified template to coherently represent the whole system. Next, it is
important to develop effective approaches to analyze the assembled network.
A network model can be subject to two types of analyses- structural and
dynamic.

3.2

Structural Analysis

A network model of biological interactions is as such a graph.

Graph-

theoretical measures can thus be used to shed light on the topological organization of the network. Local topological measures provide information
on individual nodes (e.g. node degree) while global topological measures
provide information on the whole network. A degree distribution is a useful property to measure. In particular the node(s) with the highest degree,
which upon removal can break the network down into multiple clusters.

13

3.3

Dynamic Analysis

Time can be easily incorporated into a Boolean network model. Each node
has its Boolean function. That function is evaluated to get the updated value
(state) of the node.
St+1 (i) = fi (S(t))

(3.1)

where St+1 (i) is the state of the ith node at time (t + 1) and fi is the Boolean
function for that node. S(t) is the vector of states of all N nodes.

The update paradigm can be of two types:

1. Synchronous: In synchronous update paradigm, it is assumed that
all species update simultaneously. In other words, the time scales of
all reactions in the signaling network are assumed to be equal. This
is of course, not accurate. Time scales of reactions can vary from
a few seconds to a few hours. In that sense, synchronous update is
deterministic. The synchronous paradigm is computationally efficient,
but it gives rise to spurious cycles. [9]
2. Asynchronous: To overcome the time scale drawback of synchronous
paradigm, asynchronous algorithms are used. Knowing time scale data
of some reactions, a metric can be assigned for each reaction, so that it
updates at time steps which are multiples of its metric. This is called
a deterministic asynchronous algorithm. Other algorithms include random order asynchronous, general asynchronous, etc. Asynchronous
simulations are computationally exhaustive, especially for larger bio14

logical systems, however they are able to replicate a wider range of

biological behaviours.

3.4

Network Reduction

In a Boolean framework, the number of possible states of a network (the state

space) is 2N where N is the number of nodes. Hence, it becomes impossible
to map entire state transition graph for networks of large size. In such cases
it is beneficial to reduce the number of nodes while keeping the essential
biological features intact. For example, nodes which have both in-degree and
out-degree equal to 1 can be clubbed with their respective preceding nodes.
This reduces the actual number of nodes (and hence the state space) in the
model but does not alter the models essence. some nodes attain the same
state irrespective of update method or initial condition. Such nodes can be
determined and removed.

3.5

Simulations

Simulation of Boolean network aims at generating a state transition graph.

An example simulation of a dummy network is included in Appendix. In the
following simulations we have implemented a synchronous update protocol
for the Boolean network model since the focus was on finding steady states
and limit cycles. Various kinds of asynchronous protocols can however be
implemented easily. Synchronous update protocols are prone to generating
spurious cycles [9], however steady states found using both protocols are the

15

same.

3.6

Initialization

Synchronous update algorithm evaluates states of all species at time step

t+1 using old values for all updates, that is, values at time step t. Hence it
requires initialization of all nodes at t = 0. We randomly assign a value of 0
to each node with half probability.

3.6.1

Housekeeping Constraint

From literature we have knowledge of the initial state of some species. Some
constitutive proteins are known to be present in high concentrations, also
called Housekeeping species. We found 114 such species and added the constraint of keeping these nodes equal to 1 during initialization.

3.7

Simulations in MATLAB

There are many softwares for the purpose of Boolean simulations like BooleanNet(Python) , SimboolNet(Cytoscape plugin) , GINsim, etc. However, for
a large network, these softwares provided less flexibility. Hence, a set of
MATLAB codes was written for the dynamic simulations with algorithms
to detect steady states and cyclic attractors with filters for repeated steady
states/ limit cycles.

16

Finding all attractors of the dynamics of large size networks (e.g.TNF-330 nodes) is a herculean task. But simulating this way we can get as
many attractors as required, forming a fairly random sample. The results
obtained here are then subject to various analysis methods. The algorithm
of synchronous simulations is given below.
1. State of the network is stored as a vector, S of dimension N 1.
2. To generate an initial state of the network, we first fix the values of all
Housekeeping nodes to 1.
3. The complete state of the network at S(t = 0) , S0 is generated using
a random number generator for the rest of the nodes.
4. Update equations are written in the form of a function file. The input
to that file is S(t) and the output is S(t+1)
5. State vectors after each time step are stored in a matrix, STG (State
transition graph) with the first column being S0 , second S1 and so on.
6. At each update step, we check if S(t+1) is equal to any column of the
matrix STG. If S(t+1)=S(t), it is a steady state. Else if S(t+1) is
equal to any other column, it is a cycle.
7. If S(t+1) is not equal to any column in STG, we store S(t+1) in STG
and move to the next iteration, till an attractor is reached.

17

Chapter 4
Methods of Quantitative
Analysis of Attractors
4.1

Analysis of Distance

We can hypothesize that each attractor represents a functional state of the

cell. It is useful to have a metric to measure the distance between two
attractors. We have used two types of distances:
1. min-Hamming distance:
Min-Hamming distance between two attractors is the minimum number
of nodes that must be flipped so as to change the state of the network
directly from one attractor to another. In other words, it is the number
of nodes which do not have the same state in both attractors.
2. Euclidean distance:
Considering a state of the network as an n 1 vector, the Euclidean

18

distance between two attractors is

v
u n
uX
d(Ai Aj ) = t (vik vjk )2

(4.1)

k=1

where vi is the attractor state Ai represented as a vector.

4.2

Classification

The main aim of this project is to be able to identify ways to increase networks disposition to one of the end results (apoptosis) over the other (proliferation). To enable this, we must first identify markers which differentiate
a apoptosis-bound cell phenotype from that which is proliferation-bound.

Caspase 8 is known for its role in initiation of apoptosis, but it is also

required in non-apoptotic roles.

The role of caspase 8 along with Fas-

associated death domain (FADD), FLICE like inhibitory protein (FLIP),

receptor-interacting protein kinase 1 and 3 (RIPK1, RIPK3) was reconciled
with some previous findings by [12].

Following ligation of TNF Receptor, RIPK1 is recruited to form a receptor complex. This complex-I activates NF-B transcription. FLIP is a
transcriptional target of NF-B whose upregulation is responsible for the
non-apoptotic phenotype witnessed upon TNF ligation in most cell types.
[12] FLIP forms a heterodimer with caspase-8 and inhibits the downstream
activation of RIPK3 by RIPK1. If FLIP is blocked, TNF signalling follows

19

the caspase 8 induced pro-apoptotic pathway. In the absence of caspase-8

however, RIPK1-RIPK3 signalling proceeds unchecked resulting in RIPK3
dependent programmed necrosis.

To summarize,
a High levels of FLIP: RIPK1-RIPK3 signalling inhibited by caspase 8FLIP heterodimer, leads to cell survival.
b Low levels of FLIP: caspase 8 activation proceeds unchecked, leads to
apoptosis.
c No caspase 8: RIPK3 induced programmed necrosis.

4.3

Stability Analysis

Similar to stability analysis of steady states in other mathematical modelling paradigms, stability of steady states and limit cycles can be checked
in Boolean networks.

4.3.1

Steady State Stability

The steady states obtained from Boolean simulations are subject to perturbation, and the resulting perturbed state is dynamically simulated till it
reaches a steady state. Perturbation of an attractor Ai is done as follows.
Only one node Ai (j),j (1, N ) of the state is flipped at a time. Input
nodes, i.e. nodes which only have outgoing edges are not flipped, since
20

they will always transition to a new attractor. Hence, for each attractor,
we will have N perturbed states Aip

Aip (j) = NOT(Ai (j))

(4.2)

The perturbed state Aip is then subjected to dynamic simulation as an

input state.
The resulting steady state/limit cycle is studied. A transition probability is calculated based on fractions of the N perturbations of Ai
returning to the same steady state or reaching a different steady state
or limit cycle.
Essentially, we study the dynamics of a subset of state space falling in the
region of unit Hamming distance from an attractor. The transition probabilities thus help us define the shape of the basin around the attractor. If each
perturbation returns to the same attractor, we can conclude it is a completely
rounded basin.

4.3.2

Asynchronous Markovian perturbation

Synchronous Boolean framework does not account for the stochasticity that
is possible in state transitions. Markov processes have been used to analyze
gene regulatory networks[3]. Kervizic and Corcos (2008) [9] have described a
methodology that computes the stability of cycles. A set of cycles is chosen
as the state space for this analysis. Let S be the result of simulations. S is
a set of cyclic attractors, and C is a cycle having k states {s1 , s2 , s3 , . . . , sk }.
21

Each state in C, si is perturbed by sequentially reevaluating each species by

its own Boolean function one at a time, hence asynchronous.

It is possible that in asynchronously triggering Node i, si will not change

its state. The set of all input nodes will not be a part of this triggering since
they do not update. This is similar in methodology to steady state stability
analysis, only differing in the perturbation strategy. Here for each C S
having k states,

sip (j) = fj (X(t)), j (1, N )&i (1, k)

(4.3)

Thus each cycle C gives rise to Nk perturbed states. These Nk states are
simulated synchronously until they reach attractors. Again, as computed in
stability analysis of steady states, we compute fractions of kN perturbations.

22

Chapter 5
Case Study Results
5.1

Modeling TNF- Network

The signaling network of Tumor Necrosis Factor - was constructed from

various studies available in literature. The representation was drawn using
CellDesigner. Figure 3.1 provides a flowchart of the procedure used for construction of TNF- network. 330 nodes take part in the complex network, of
which 216 nodes have Boolean equations associated with them. Hence, the
rest 114 nodes are all input nodes, with only outgoing edges. The Boolean
update rules for the 216 nodes were constructed by combining a subset of
330 nodes using logical operators AND, OR or NOT.
Next we study the set of nodes with housekeeping constraints (section
3.6.1). Of 114 housekeeping nodes, 84 are input nodes. Hence, these nodes
are effectively always ON in any simulation at any time step. Hence the
initialization procedure for TNF- network is described in Table 5.1

23

Figure 5.1: Flowchart for constructing Signaling Networks

SET

Input nodes

Non-input nodes

Type

TOTAL

SET A

30

84

constrained

114

SET B

84

132

randomized

216

TOTAL

114

216

330

Table 5.1: Sets of nodes randomized or constrained while initializing

24

5.2
5.2.1

Distance Analysis
min-Hamming Distance

Figure 5.2: Distribution of Hamming distances for a set of attractors

Figure 5.2 shows the distribution of Hamming distance between pairs of
steady states. On an average, the distance between two attractors is approximately 80 nodes, that is, two attractors have on an average 80 nodes (out
of 330) differing in states.

25

5.3

Classification

The dynamics of a network goes through many states. While non-attractor

states are visited in a transient fashion, attractors are visited often and from
multiple paths. Attractors are also independent of the update paradigm
used, and hence can be identified with phenotypes. Phenotypes of interest
to us for the TNF- network are: Apoptosis and Survival. The markers
for phenotypes are described in section 4.2. Accordingly, we classify steady
states with respect to the states of the marker nodes.
CASPASE-8

FLIP

Necrosis

Apoptosis

Survival

Necrosis

Phenotype

Table 5.2: Truth table for phenotype based classification of steady states
Of the 9638 steady states available, 45% (4411) attractors identify with
the apoptosis phenotype markers while the rest (5227) fall under the survival
category.

5.4

Stability Analysis

5.4.1

Perturbation analysis for steady states

Following the procedure listed in section 4.3, all steady states were subject
to unit perturbations per node. The distributions of transition fractions is
shown in Figure 5.3. The results for about 9600 steady states are obtained
as follows
26

 For 90 % of the steady states (approx. 8500) the results are the same.
37% of 216 unit perturbations (79) return to the same steady state and
the rest 63% take up new steady states.
The set of 79 (and hence rest 137) nodes is also the same for these 8500
attractors.
The remaining 10% attractors show different results.
We verified the possibility that the 8500 steady states might have the
same states for this set of 79 nodes, and vary only in the states of the
rest. It is a possibility since the set of 8500 states can easily fall in the
2137 state sub-space. However, that is not the case.

5.4.2

Asychronous Markovian perturbation for cyclic

attractors

Following the procedure in section 4.3.2, the set of cyclic attractors obtained
from synchronous simulations was analysed. It follows that input nodes
(nodes with outgoing edges only) will not be a triggered since they do not
have an update function. Thus we trigger each of the 216 updating nodes
asynchronously. The results obtained are shown in figure 5.4.
Transition fraction returning to the same cycle is greater than 0.9 for
88% of state cycles.
The same transition fraction is equal to 1 for 23% of state cycles

27

Figure 5.3: Histograms for transition fractions in TNF steady state stability
analysis

28

Figure 5.4: distribution of transition fractions returning to the same state

for asynchronous perturbations
State cycles which have all perturbations transitioning back to the same
cycle are termed as absorbing states. Other states are concluded to be
spurious. [9]

5.5

Phenotype switch

Having classified the steady state attractors of TNF- network, we look at

the possibility of phenotype switching. The procedure is same as the previous
section, however, the set of attractors classified under the Survival category
is used in stead of the whole set of attractors. At each perturbation, we check
29

against the classification markers and note if the new steady state matches
the markers of the switched phenotype, i.e. apoptosis. It is interesting to note
that for 5227216 independent perturbations, not one incident of phenotype
switch is observed. The same computation done with the set of attractors
classified under apoptosis also yielded no instances of phenotype switch. It
follows that all the unit-perturbed states of both sets fall in the basin of
attraction of the respective phenotypes.

5.6

Toll-Like Receptor (TLR) Network

We have access to many curated signal transduction networks, and our lab
members have developed codes to generate Boolean equations from graphs.
One such network is that of Toll-like receptor. TLR networks Boolean model
was simulated synchronously to get attractors. The stability analysis described in section 4.3 was performed on steady state attractors of TLR network as well.
Figure 5.5 shows the transition fractions obtained from stability analysis. Subplots 1 and 2 show histograms of transition fractions to other
steady states and limit cycles respectively.
For 92% of the 2460 steady states subject to this analysis, we have
obtained a transition fraction of 95% (of 1229) per attractor.
Rest of the transitions all occur to limit cycles.
For all 2460 1229 perturbations, the transition back to same steady
state is 0.
30

Figure 5.5: The two plots show a histogram of transition fractions upon
producing unit perturbations. TLR network has 1229 nodes. 2460 steady
states were studied. x-axis is number of nodes as a fraction of 1229. Y- axis
is the number of times (out of 2460) that a particular fraction was obtained.
subplot 1 is for transitions to other steady states, subplot 2 is for transitions
to limit cycles. For the set of steady states studied, fraction of transitions
coming back to the same steady states is 0.

31

Chapter 6
Conclusions and future work
From the examples of TNF- and TLR networks, we can see that we have
developed a methodology to model and simulate Boolean networks to obtain
attractors: point as well as cycles, and examine their stability. This methodology can be applied to any known network, and we may observe systemic
properties of signaling networks in general. Since attractors may be correlated with phenotypes, this methodology can be extended to finding domain
of attraction of a particular phenotype.

Future Work With the study of random networks, we found that it takes
approximately 50% node flips to leave a particular attractors basin and reach
another attractor. Though degree distributions of random networks and biological networks are significantly different, it is a fair result that a unit node
flip does not result in a switch from one phenotypes basin of attraction to
another. Seeing as real networks have a degree distribution that is scale free
as opposed to a Poissonian for random networks [1], we can fairly predict

32

that the number of node flips, on an average, will not be as high as 50% to
switch phenotype. It is then an interesting problem to identify, for a first,
a single instance of phenotype switch, and eventually to identify an optimal
set of nodes key to switch from survival phenotype to apoptosis.

Synchronous simulation is computationally efficient, but wrong in its assumption of equal time scales of all reactions. Incorporating time-scales of
different reactions, i.e. a deterministic asynchronous algorithm, will generate
biologically more relevant attractors since it represents dynamics of a signaling network more accurately than a simple synchronous algorithm.

As of now, we are scanning a large state space. However, the network

can be simplified by removing particular nodes and interactions, without
affecting the biological model. This procedure will require manual curation,
but a reduced network will increase computational efficiency.

33

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36

Appendices

37

Appendix A
A simulation example:
TOYNET
Figure A.1 shows a sample interaction hypergraph with signed and directed
edges. The model equations for TOYNET can be written as follows:
A(t+1) = NOT D(t)
B(t+1) = A(t) AND I1(t)
C(t+1) = B(t) OR E(t)
D(t+1) = C(t)
E(t+1) = NOT I1(t) AND I2(t)
F(t+1) = E(t) OR G(t)
G(t+1) = F(t)

We have 9 nodes and 7 Boolean functions. Nodes I1 and I2 are input

nodes, they will not be updated. The state vector
S(t)=[I1(t) I2(t) A(t) B(t) C(t) D(t) E(t) F(t) G(t)]
38

Figure A.1: Interaction hypergraph of a sample network TOYNET

keeps track of the state of the network. The network size is small, so is
the state space (29 = 512). A state number can be assigned to each vector,
which is the decimal counterpart of the binary number formed by S(t). For
example,
S = [1 0 0 0 0 1 1 0 0] will be termed State-268.
1. Initialize S randomly.
2. Calculate state number.
3. Obtain S(t+1) from S(t) from the Boolean equations
4. Update till an attractor is reached
Say S(0) = [1 0 1 1 0 1 0 0 1] or 361 (hereafter referred to by state number).
The state transitions which occur are: 361 53 89 381 125 125
hence state 125 is an attractor.
39

Appendix B
Identifying unsteady part of
network
Initially, synchronous simulations would yield only limit cycles of length 4 for
all inputs. Hence, we estimated there must be a continuously cycling part of
the network. To detect that, we ran a simulation for all cycles which would
detect nodes which were changing their value from one state in a cycle to
another. The set of cycles C consists of m cycles {c1 , c2 , . . . , cm }of varying
lengths {l1 , l2 , . . . , lm ,}. For each ci , ci (x) ci (x + 1) is computed and those
nodes for which this difference is not zero are noted for all x (1, li ). Thus we
can compute the frequency with which a particular node is changing states
in a set of cycles.

40

Figure B.1: This shows a frequency bar graph for a set of 500 cycles, with frequency of appearance of a node plotted against node number. As is evident,
4 nodes are changing states in each of the 500 cycles.
We infer from the above bar chart that these 4 nodes are responsible for
the unsteady behaviour of the network. They are all connected and form a
part of the network which cannot attain steady state for any input values.
This part was later modified to reflect correct biological behavior. As can be
seen from figure B.2, this part of the network does not have a steady state
for any combination of inputs.

41

Figure B.2: Part of TNF network responsible for unsteady behaviour

42

Appendix C
TNF pathway

Figure C.1: Figure shows a part of TNF- signaling network in CellDesigner

43

Appendix D
List of Interactions
Table D.1: Table of Interactions in TNF- signaling

Target

Boolean Equation

Node
SA39

SA40 |(SA31 & SA42 & SA539 ) |(SA31 & SA45 )

SA137

(SA136 & SA135 ) |(SA136 & SA177 ) |(SA136 & SA27 )

SA141

SA140 & SA139 & (SA688 |SA700 )

SA134

CSA2 |(SA133 & SA132 ) |(SA133 & SA156 ) |(SA133 &

SA292 )

SA152

(CSA31 & SA291 ) |(CSA31 & SA151 )

SA158

(SA159 & SA291 ) |(SA159 & SA135 ) |(SA159 & SA154 )

SA161

(SA162 & SA291 ) |(SA162 & CSA31 )

CSA31

(SA145 & SA149 ) |(SA145 & SA150 )

SA222

(CSA36 & SA220 ) |(CSA36 & SA445 & SA58 & SA125 )

SA223

(CSA36 & SA220 ) |(CSA36 & SA445 & SA58 & SA125 )

44

SA451

(SA450 & SA126 ) |(SA450 & SA127 ) |(SA450 & SA130 )

SA129

(SA530 ) |(SA291 ) |(SA128 & SA92 & SA90 ) |(SA128

& SA21 ) |(SA128 & SA51 )

SA58

(SA59 & SA21 ) |(SA59 & SA57 )

SA125

(SA92 ) |(SA124 & SA106 ) |(SA124 & SA21 ) |(SA124 &

SA51 )

SA73

(SA72 & SA65 ) |(SA72 & SA71 )

SA92

(SA88 & SA100 ) |(SA88 & SA102 )

SA91

(SA87 & SA77 ) |(SA87 & SA100 & SA102 )

CSA19

(CSA20 & SA31 ) |(CSA20 & SA76 ) |(CSA20 & SA84 &
SA58 )

SA117

(SA116 & SA115 ) |(SA116 & SA179 )

CSA22

SA108 |CSA15

SA254

SA243 |SA256

SA263

SA256 |SA284

SA276

SA243 |SA284

SA272

SA256 |SA284

SA146

SA141 |SA142

SA154

SA152 |SA157

SA250

SA247 |SA252 |SA249 |SA268 |SA266 |SA271 |SA246

|SA251 |SA255 |SA257 |SA260 |SA262 |SA261 |SA264
|SA267 |SA265 |SA269 |SA270 |SA143 |SA147

SA568

SA567 |SA585

SA572

SA571 |SA608 |SA609 |SA607

SA291

SA146 |SA144

45

SA701

CSA3 |SA135

SA208

SA205 |SA202 |SA129

SA77

SA539 |SA113 |(SA74 & CSA5 )

SA176

SA21 |(SA175 & SA174 )

SA31

SA135 |SA113 |(CSA3 & SA667 & SA38 )

SA38

SA42 |SA113 |(SA37 & SA97 & SA58 )

SA452

(SA451 & SA126 ) |(SA451 & SA130 )

SA491

(SA492 & SA500 ) |(SA492 & SA503 )

SA49

SA125 |(SA48 & SA47 )

SA57

SA533 |(SA55 & SA56 & SA21 )

CSA29

SA676 |SA677 |SA594 |(CSA27 & SA119 )

SA106

SA125 |(SA105 & CSA11 )

CSA18

SA113 |(CSA19 & SA76 & SA102 )

SA112

SA113 |(SA111 & CSA5 )

SA273

SA284

SA245

SA243

SA281

SA284

SA253

SA284

SA274

SA284

SA282

SA284

SA287

SA284

SA279

SA284

SA275

SA243

SA280

SA284

46

SA244

SA243

SA248

SA243

SA542

SA539

SA294

SA539

SA135

SA134

SA144

SA141

SA145

SA141

SA143

SA141

SA147

SA141

SA138

SA136 & SA129

SA139

SA137

SA19

SA18 & CSA1

SA142

SA138

SA148

SA151 & SA58

SA157

SA158

SA156

SA155 & SA157

SA21

SA20 & SA23

SA160

SA161

SA153

SA154 & SA125

SA163

SA156

SA23

SA22 & SA11

SA173

SA172 & SA17

SA174

SA173

SA179

SA180 & SA176

47

SA177

SA178

CSA33

CSA32

SA178

CSA33 & SA179

SA175

CSA33 & CSA1 & SA132 & SA135 & SA160

SA25

SA24 & SA157

SA27

SA26

SA26

SA25 & SA19

CSA3

CSA1 & CSA2 & SA28 & SA29 & SA32

SA34

SA33 & CSA1

SA220

SA221 & SA222

SA32

SA31 & SA34

SA284

SA157

SA243

SA163

CSA1

SA2 & SA5

SA249

SA259 & SA284

SA258

SA259 & SA284

SA268

SA283 & SA284

SA36

SA35 & SA174

SA37

SA36

SA256

SA160

SA289

SA288 & SA129

SA35

CSA3

SA98

SA208

SA45

SA44 & CSA1

48

SA292

SA294

SA293

SA294

SA444

SA443 & SA446

SA445

CSA15

SA446

SA445

SA448

SA447 & SA130 & SA127

SA449

SA448 & SA130

SA453

SA452 & SA126

SA455

SA454 & SA126

CSA54

CSA52 & SA471

CSA55

CSA53 & SA471

CSA52

SA453 & SA470

CSA53

SA455 & SA470

SA486

SA485 & SA127 & SA126

SA485

SA484

SA492

SA493 & SA130

SA42

SA43 & CSA18

SA490

SA491 & SA500

SA489

SA490 & SA503

SA500

SA109

SA502

SA501 & SA58

SA503

SA502

CSA56

SA494 & SA492 & SA449

SA47

SA46 & CSA1

49

SA2

SA1

SA539

SA538 & SA129

SA540

SA542

SA541

SA540 & SA130

CSA57

SA486 & SA541

SA51

SA50 & CSA1

SA560

SA562

SA561

SA560 & SA503

SA56

SA53 & SA49

CSA59

SA569 & SA568

SA570

CSA59

SA571

SA570

SA565

CSA58 & SA268

SA567

SA566 & SA565

SA566

SA559

SA577

SA550

SA578

SA558

CSA58

SA577 & SA578

SA581

CSA61 & CSA60

SA582

CSA61 & CSA60

CSA60

SA560 & SA580

SA595

SA596 & SA126

SA594

SA595 & SA503

SA59

SA58 & SA61

50

SA607

SA603

SA608

SA604

SA609

SA605

SA61

SA60 & SA11

SA615

SA616

SA614

SA130 & SA615

SA128

SA614

SA63

SA62 & SA57

SA65

SA64 & SA68

SA616

SA208

SA662

SA660 & SA125 & SA38

SA667

SA665 & SA663

SA663

SA662

SA68

SA69 & SA63

SA8

SA9 & CSA1

SA29

SA146

SA676

SA533

SA677

SA288

SA71

SA70 & SA38

SA688

SA288

SA606

SA563

CSA17

SA288

SA700

SA223

CSA5

CSA6 & SA29 & SA31

51

CSA4

CSA5 & SA123

SA89

SA85 & SA100

SA76

SA75 & SA77

SA84

SA80 & SA77 & SA38

SA104

SA92 & SA58

SA7

SA6 & SA8

SA90

SA86 & SA102

SA81

SA84 & CSA19

CSA9

SA93 & SA94

SA97

SA96 & SA17

CSA11

CSA8 & SA23

SA96

SA97 & SA61

CSA7

CSA9 & SA65 & SA56

CSA12

CSA10 & SA445

SA11

SA10 & SA7

CSA8

CSA7 & SA97

CSA10

CSA11 & SA125

SA100

SA99 & SA38

SA99

SA98

SA102

SA73 & SA31

CSA20

CSA14 & SA29 & SA112

CSA16

CSA17 & CSA18

CSA15

CSA16 & CSA25

CSA23

CSA15

52

CSA24

CSA23 & CSA18

CSA21

CSA24 & SA445

CSA26

CSA21 & SA109

SA111

SA110

SA115

SA114 & SA31

SA119

SA118

CSA27

CSA30 & SA120

CSA30

CSA28 & SA444

CSA28

CSA26 & SA565

SA15

SA14 & CSA1

SA120

SA117

SA118

SA121 & SA123 & SA125

SA123

SA122 & SA89 & SA91

SA127

SA123

SA126

SA125

SA130

SA129

SA132

SA131 & CSA3

SA17

SA16 & SA15

Table D.2: Index of Species Alias used in Table D.1

Species

Species Name

Alias

53

CSA1

TNF-R1-STNF ALPHA BR COMPLEX COM ACT

C1-OUT CRD2 SIM PLAD SIM STNF ALPHA PRO

CSA10

ACT MULTI TNF-R1 PRO ACT MULTI CRD3 SIM

RAF COMPLEX COM C1-INS 14-3-3 PRO ACT B-RAF
PRO PHO PHO CRAF/RAF-1 PRO ACT EMP PHO

CSA11

PHO PHO PHO PHO

RAF COMPLEX COM ACT C1-INS CRAF/RAF-1 PRO
ACT EMP PHO PHO PHO PHO PHO PHO B-RAF PRO

CSA12

ACT PHO 14-3-3 PRO ACT

RAF COMPLEX COM C1-INS 14-3-3 PRO ACT B-RAF
PRO PHO PHO CRAF/RAF-1 PRO PHO PHO PHO

CSA14

PHO PHO PHO

IKK COMPLEX COM C1-INS IKK ALPHA BR IKK1
PRO EMP EMP MULTI IKK BETA BR IKK2 PRO EMP
EMP MULTI IKK GAMMA BR NEMO PRO EMP
MULTI ELKS PRO ACT HSP 90 PRO ACT MULTI

CSA15

CDC37 PRO ACT

NF- KAPPA B-I KAPPA B-PKA COMPLEX COM
C1-INS NF- KAPPA B COM I KAPPA B COMPLEX

CSA16

COM PKAC PRO

NF- KAPPA B-I KAPPA B-PKA COMPLEX COM
C1-INS I KAPPA B COMPLEX COM NF- KAPPA B

CSA17

COM PKAC PRO

NF- KAPPA B-I KAPPA B-PKA COMPLEX COM
C1-INS I KAPPA B COMPLEX COM ACT NF- KAPPA
B COM PKAC PRO P65/RELA PRO

54

CSA18

IKK COMPLEX COM ACT C1-INS ELKS PRO ACT

HSP 90 PRO ACT MULTI CDC37 PRO ACT IKK
GAMMA BR NEMO PRO ACT UBI MULTI IKK BETA
BR IKK2 PRO ACT PHO PHO MULTI IKK ALPHA BR

CSA19

IKK1 PRO ACT PHO PHO PHO MULTI

IKK COMPLEX COM C1-INS IKK BETA BR IKK2
PRO EMP EMP MULTI IKK ALPHA BR IKK1 PRO
ACT PHO PHO PHO MULTI IKK GAMMA BR NEMO
PRO ACT UBI MULTI ELKS PRO ACT HSP 90 PRO

CSA2

ACT MULTI CDC37 PRO ACT

TRAF1/2 COMPLEX COM C1-INS TRAF 2 PRO TRAF

CSA20

1 PRO
IKK COMPLEX COM C1-INS IKK ALPHA BR IKK1
PRO EMP EMP MULTI IKK BETA BR IKK2 PRO EMP
EMP MULTI IKK GAMMA BR NEMO PRO ACT UBI
MULTI ELKS PRO ACT HSP 90 PRO ACT MULTI

CSA21

CDC37 PRO ACT

NF- KAPPA B COM C1-INS P50 PRO ACT P65/RELA

CSA22

PRO PHO PHO

I KAPPA B COMPLEX COM C1-INS I KAPPA B
ALPHA PRO PHO PHO UBI UBI I KAPPA B BETA

CSA23

PRO PHO PHO UBI

NF- KAPPA B COM C1-INS P65/RELA PRO P50 PRO

CSA24

NF- KAPPA B COM C1-INS P65/RELA PRO PHO P50

CSA25

PRO ACT
(SCF)-TYPE E3 COM ACT C1-INS CUL1 PRO ACT
SKP1 PRO ACT
55

CSA26

NF- KAPPA B COM C1-INS P50 PRO ACT P65/RELA

CSA27

PRO PHO PHO PHO

NF- KAPPA B COM C2-INS P50 PRO ACT P65/RELA
PRO PHO PHO PHO PHO UBI CREB/P300 PRO ACT

CSA28

PHO
NF- KAPPA B COM C2-INS P50 PRO ACT P65/RELA

CSA29

PRO PHO PHO PHO

NF- KAPPA B COM ACT C2-INS P50 PRO ACT
P65/RELA PRO ACT PHO PHO PHO PHO UBI
CREB/P300 PRO ACT PHO

CSA3

TRADD COMPLEX COM ACT C1-INS TRAF1/2-CIAP

COMPLEX COM TRADD PRO RIP PRO CIAP1/2 PRO

CSA30

NF- KAPPA B COM C2-INS P50 PRO ACT P65/RELA

PRO PHO PHO PHO UBI CREB/P300 PRO ACT PHO

CSA31

APOPTOSOME COM ACT C1-INS APAF-1 PRO ACT

CSA32

DATP SIM CYTOCHROME C PRO ACT

CTSD COMPLEX COM C3-INS PRO-A-SMASE PRO

CSA33

PRE-PRO-CTSD PRO
CTSD COMPLEX COM C4-INN PRE-PRO-CTSD PRO

CSA36

PRO-A-SMASE PRO
BCL-BAD BR COMPLEX COM C1-INS BCL-XL PRO

CSA4

BAD PRO ACT

TAB COMPLEX COM C1-INS TAB1 PRO PHO PHO
TAB2 PRO ACT PHO PHO PHO TAB3 PRO PHO PHO

CSA41

PHO
TRAF1/2-CIAP COMPLEX COM TRAF 1 PRO TRAF 2
PRO

56

CSA42

I KAPPA B COMPLEX COM I KAPPA B ALPHA PRO

PHO PHO UBI UBI I KAPPA B BETA PRO PHO PHO

CSA43

UBI
NF- KAPPA B COM P50 PRO P65/RELA PRO

CSA44

NF- KAPPA B COM P65/RELA PRO P50 PRO

CSA45

I KAPPA B COMPLEX COM I KAPPA B BETA PRO

CSA46

PHO PHO I KAPPA B ALPHA PRO PHO PHO

NF- KAPPA B COM P50 PRO

CSA47

I KAPPA B COMPLEX COM ACT I KAPPA B ALPHA

PRO ACT EMP EMP I KAPPA B BETA PRO ACT

CSA5

EMP EMP
TAB COMPLEX COM ACT C1-INS TAB1 PRO ACT

CSA52

TAB2 PRO ACT PHO PHO TAB3 PRO ACT EMP EMP
TCF-SRECOMPLEX COM C2-INS SRE PRO ACT

CSA53

ELK-1 PRO ACT PHO PHO PHO PHO PHO

SAP1A-SRE COMPLEX COM C2-INS SAP-1A PRO

CSA54

ACT PHO PHO PHO PHO SRE PRO ACT

TCF-SRE-SRF COMPLEX COM ACT C2-INS SRE PRO
ACT ELK-1 PRO ACT PHO PHO PHO PHO PHO SRF

CSA55

PRO ACT
SAP1A-SRE-SRF COMPLEX COM ACT C2-INS SRE
PRO ACT SAP-1A PRO ACT PHO PHO PHO PHO SRF

CSA56

PRO ACT
TRE COMPLEX COM ACT C2-INS TRE PRO ACT
ATF-2 PRO ACT PHO PHO PHO C-JUN PRO ACT
PHO PHO PHO PHO

57

CSA57

AP1 COM ACT C2-INS C-FOS PRO ACT PHO PHO

CSA58

PHO PHO C-JUN PRO ACT PHO PHO PHO PHO

P53-MDM-2 COMPLEX COM ACT C2-INS MDM-2

CSA59

PRO ACT P53 PRO

CYCLIN E-CDK2 COMPLEX COM C2-INS CDK2 PRO

CSA6

ACT CYCLIN E PRO ACT

TAB COMPLEX COM C1-INS TAB1 PRO TAB2 PRO

CSA60

TAB3 PRO
CYCLIN D1-CDK4 COMPLEX COM ACT C2-INS

CSA61

CYCLIN D1 PRO ACT CDK4 PRO ACT

RB COMPLEX COM ACT C2-INS RB PRO ACT E2F

CSA7

PRO DP1 PRO ACT

RAF COMPLEX COM C1-INS B-RAF PRO ACT PHO
CRAF/RAF-1 PRO EMP PHO PHO PHO 14-3-3 PRO

CSA8

ACT
RAF COMPLEX COM C1-INS CRAF/RAF-1 PRO EMP
PHO PHO PHO PHO PHO B-RAF PRO ACT PHO

CSA9

14-3-3 PRO ACT

RAF COMPLEX COM C1-INS CRAF/RAF-1 PRO EMP
PHO PHO 14-3-3 PRO ACT B-RAF PRO 14-3-3 PRO

SA1

ACT
TNF-R1 PRO C1-OUT

SA10

SPHINGOMYELIN SIM C1-OUT

SA100

ASK1 PRO ACT PHO PHO C1-INS

SA102

MEKK1 PRO ACT PHO PHO PHO PHO C1-INS

SA104

MKK4/JNKK1/SEK1 PRO PHO PHO C1-INS

SA105

MEK1/2 PRO C1-INS

58

SA106

MEK1/2 PRO ACT PHO PHO C1-INS

SA107

IKB DEG C1-INS

SA108

26S PROTEOSOME PRO ACT C1-INS

SA109

CK II PRO ACT C1-INS

SA11

CERAMIDE SIM C1-INS

SA110

TRAF6 PRO C1-INS

SA111

TRAF6 PRO EMP MULTI C1-INS

SA112

TRAF6 PRO ACT UBI MULTI C1-INS

SA113

CYLD PRO ACT C1-INS

SA114

P62 PRO C1-INS

SA115

P62 PRO ACT C1-INS

SA116

PKC ZETA PRO C1-INS

SA117

PKC ZETA PRO ACT PHO C1-INS

SA118

MSK1/2 PRO ACT PHO C1-INS

SA119

MSK1/2 PRO ACT PHO C2-INS

SA120

PKC ZETA PRO ACT PHO C2-INN

SA121

MSK1/2 PRO C1-INS

SA122

P38 PRO EMP C1-INS

SA123

P38 PRO ACT PHO PHO C1-INS

SA124

ERK1/2 PRO C1-INS

SA125

ERK1/2 PRO ACT PHO PHO C1-INS

SA126

ERK1/2 PRO ACT PHO PHO C2-INS

SA127

P38 PRO ACT PHO PHO C2-INS

SA128

JNK 1 PRO EMP C1-INS

59

SA129

JNK 1 PRO ACT PHO PHO C1-INS

SA130

JNK 1 PRO ACT PHO PHO C2-INS

SA131

FADD PRO C1-INS

SA132

FADD PRO ACT C1-INS

SA133

PROCASPASE 8 PRO C1-INS

SA134

CASPASE 8 BR (MACH COMMA FLICE COMMA BR

MCH5 ) PRO DON C1-INS

SA135

CASPASE 8 BR (MACH COMMA FLICE COMMA BR

MCH5 ) PRO ACT DON MULTI C1-INS

SA136

BID PRO C1-INS

SA137

TBID PRO ACT DON C1-INS

SA138

JBID PRO ACT C1-INS

SA139

TBID PRO ACT DON C5-INS

SA14

PC-PLC PRO C1-OUT

SA140

BAX/BAK PRO C5-INS

SA141

BAX/BAK PRO ACT MULTI C5-OUT

SA142

JBID PRO ACT C5-INN

SA143

AIF PRO ACT C1-INS

SA144

OMI/HTRA2 PRO ACT C1-INS

SA145

CYTOCHROME C PRO ACT C1-INS

SA146

SMAC/DIABLO PRO ACT C1-INS

SA147

ENDOG PRO ACT C1-INS

SA148

PROCASPASE 9 PRO PHO C1-INS

SA149

APAF-1 PRO ACT C1-INS

SA15

PC-PLC PRO ACT C1-INN

60

SA150

DATP SIM C1-INS

SA151

PROCASPASE 9 PRO ACT EMP C1-INS

SA152

CASPASE 9 BR ( ICE-LAP6 COMMA BR MCH6) PRO

SA153

DON C1-INS
CASPASE 9 BR ( ICE-LAP6 COMMA BR MCH6) PRO

SA154

DON DON PHO MULTI C1-INS

CASPASE 9 BR ( ICE-LAP6 COMMA BR MCH6) PRO

SA155

ACT DON DON EMP MULTI C1-INS

PROCASPASE 6 PRO C1-INS

SA156

CASPASE 6 BR (MCH2 ALPHA ) PRO DON DON DON

SA157

C1-INS
CASPASE 3 BR (CPP32 COMMA YAMA COMMA BR
APOPAIN) PRO ACT DON MULTI C1-INS

SA158

CASPASE 3 BR (CPP32 COMMA YAMA COMMA BR

APOPAIN) PRO DON C1-INS

SA159

PROCASPASE 3 PRO C1-INS

SA16

PC SIM C1-OUT

SA160

CASPASE 7 BR (MCH3 COMMA ICE-LAP3 COMMA

BR CMH-1) PRO ACT DON MULTI C1-INS

SA161

CASPASE 7 BR (MCH3 COMMA ICE-LAP3 COMMA

BR CMH-1) PRO DON C1-INS

SA162

PROCASPASE 7 PRO C1-INS

SA163

CASPASE 6(MCH2 ALPHA ) PRO ACT DON DON

SA17

DON MULTI C1-INS

DAG PRO ACT C1-INN

SA172

PKC DELTA PRO C1-INS

SA173

PKC DELTA PRO EMP PHO C1-INS

61

SA174

PKC DELTA PRO ACT PHO PHO C1-INS

SA175

A-SMASE PRO DON C4-TRA

SA176

A-SMASE PRO ACT DON PHO C4-INS

SA177

CATHEPSIN D PRO ACT C1-INS

SA178

CATHEPSIN D PRO ACT C4-INN

SA179

CERAMIDE SIM C4-OUT

SA18

RAIDD PRO C1-INS

SA180

SPHINGOMYELIN SIM C4-OUT

SA19

RAIDD PRO ACT C1-INS

SA2

TNF-R1 PRO MULTI C1-OUT

SA20

C1P PRO C1-INS

SA202

FHC PRO ACT C5-INS

SA205

MN-SOD PRO ACT C5-INS

SA208

ROS SIM C5-INS

SA21

C1P PRO ACT C1-INS

SA22

CAPK PRO C1-INS

SA220

BAD14-3-3 PRO C1-INS

SA221

P14-3-3 PRO ACT C1-INS

SA222

BAD PRO PHO PHO PHO C1-INS

SA223

BCL-XL PRO ACT C1-INS

SA23

CAPK PRO ACT C1-INS

SA24

PROCASPASE 2 PRO C1-INS

SA243

CASPASE 6(MCH2 ALPHA ) PRO ACT DON DON

SA244

DON MULTI C2-INS

SATB1 PRO ACT C2-INS
62

SA245

LAMIN PRO ACT C2-INS

SA246

S3734 DEG C2-INS

SA247

S3733 DEG C2-INS

SA248

AP2- ALPHA PRO ACT C2-INS

SA249

CAD PRO ACT C2-INS

SA25

CASPASE 2 BR (NEDD2 COMMA ICH-1) PRO DON

SA250

C1-INS
APOPTOSIS PHE C2-INS

SA251

S3732 DEG C2-INS

SA252

S1 DEG C2-INS

SA253

ACINUS PRO ACT C2-INS

SA254

VIMENTIN PRO ACT C2-INS

SA255

S11 DEG C2-INS

SA256

CASPASE 7 BR (MCH3 COMMA ICE-LAP3 COMMA

CMH-1) PRO ACT DON MULTI C2-INS

SA257

S12 DEG C2-INS

SA258

ICAD PRO C2-INS

SA259

DFF PRO ACT C2-INS

SA26

CASPASE 2 BR (NEDD2 COMMA ICH-1) PRO DON

SA260

DON C1-INS
S13 DEG C2-INS

SA261

S15 DEG C2-INS

SA262

S14 DEG C2-INS

SA263

GAS2 PRO ACT C2-INS

SA264

S16 DEG C2-INS

63

SA265

S17 DEG C2-INS

SA266

S22 DEG C2-INS

SA267

S18 DEG C2-INS

SA268

T PARP PRO C2-INS

SA269

S19 DEG C2-INS

SA27

CASPASE 2 BR (NEDD2 COMMA ICH-1) PRO ACT

SA270

DON DON MULTI C1-INS

S20 DEG C2-INS

SA271

S21 DEG C2-INS

SA272

FAK PRO ACT C2-INS

SA273

GELSOLIN PRO ACT C2-INS

SA274

D4-GDI PRO ACT C2-INS

SA275

NUMA PRO ACT C2-INS

SA276

DNA BR TOPOISOMERASE I PRO ACT C2-INS

SA279

SREBPS PRO ACT C2-INS

SA28

TRADD PRO C1-INS

SA280

LIM-K1 PRO ACT C2-INS

SA281

ALPHA ACTIN PRO ACT C2-INS

SA282

SLK PRO ACT C2-INS

SA283

PARP PRO ACT C2-INS

SA284

CASPASE 3 BR (CPP32 COMMA YAMA COMMA

APOPAIN) PRO ACT DON MULTI C2-INS

SA287

AP24 PRO ACT C2-INS

SA288

BCL-2 PRO ACT C1-INS

SA289

BCL-2 PRO PHO C1-INS

64

SA29

CIAP1/2 PRO ACT C1-INS

SA291

XIAP PRO ACT C1-INS

SA292

C-FLIP SUB L PRO ACT C1-INS

SA293

C-FLIP SUB S PRO C1-INS

SA294

C-FLIP PRO C1-INS

SA3

CRD3 SIM

SA31

RIP PRO ACT UBI C1-INS

SA317

CRD2 SIM

SA318

PLAD SIM

SA319

STNF ALPHA PRO ACT MULTI

SA32

RIP PRO C1-INS

SA320

TNF-R1 PRO ACT MULTI

SA321

CRD3 SIM

SA322

TRAF 2 PRO

SA323

TRAF 1 PRO

SA324

TRADD PRO

SA325

RIP PRO

SA326

CIAP1/2 PRO

SA327

TRAF 1 PRO

SA328

TRAF 2 PRO

SA329

TAB1 PRO PHO PHO

SA33

CEZANNE PRO C1-INN

SA330

TAB2 PRO ACT PHO PHO PHO

SA331

TAB3 PRO PHO PHO PHO

65

SA332

TAB1 PRO ACT

SA333

TAB2 PRO ACT PHO PHO

SA334

TAB3 PRO ACT EMP EMP

SA335

TAB1 PRO

SA336

TAB2 PRO

SA337

TAB3 PRO

SA338

B-RAF PRO ACT PHO

SA339

CRAF/RAF-1 PRO EMP PHO PHO PHO

SA34

CEZANNE PRO ACT C1-INS

SA340

14-3-3 PRO ACT

SA341

CRAF/RAF-1 PRO EMP PHO PHO PHO PHO PHO

SA342

B-RAF PRO ACT PHO

SA343

14-3-3 PRO ACT

SA344

CRAF/RAF-1 PRO EMP PHO PHO

SA345

14-3-3 PRO ACT

SA346

B-RAF PRO

SA347

14-3-3 PRO ACT

SA348

14-3-3 PRO ACT

SA349

B-RAF PRO PHO PHO

SA35

TRAF2 PRO EMP EMP C1-INS

SA350

CRAF/RAF-1 PRO ACT EMP PHO PHO PHO PHO

SA351

PHO
CRAF/RAF-1 PRO ACT EMP PHO PHO PHO PHO

SA352

PHO PHO
B-RAF PRO ACT PHO

66

SA353

14-3-3 PRO ACT

SA354

14-3-3 PRO ACT

SA355

B-RAF PRO PHO PHO

SA356

CRAF/RAF-1 PRO PHO PHO PHO PHO PHO PHO

SA359

IKK ALPHA BR IKK1 PRO EMP EMP MULTI

SA36

TRAF2 PRO PHO EMP C1-INS

SA360

IKK BETA BR IKK2 PRO EMP EMP MULTI

SA361

IKK GAMMA BR NEMO PRO EMP MULTI

SA362

ELKS PRO ACT

SA363

HSP 90 PRO ACT MULTI

SA364

CDC37 PRO ACT

SA365

PKAC PRO

SA366

I KAPPA B ALPHA PRO PHO PHO UBI UBI

SA367

I KAPPA B BETA PRO PHO PHO UBI

SA368

P50 PRO

SA369

P65/RELA PRO

SA37

TRAF2 PRO PHO UBI MULTI C1-INS

SA370

PKAC PRO

SA371

P65/RELA PRO

SA372

P50 PRO

SA373

I KAPPA B BETA PRO PHO PHO

SA374

I KAPPA B ALPHA PRO PHO PHO

SA375

PKAC PRO

SA376

P65/RELA PRO

67

SA377

P50 PRO

SA378

I KAPPA B ALPHA PRO ACT EMP EMP

SA379

I KAPPA B BETA PRO ACT EMP EMP

SA38

TRAF2 PRO ACT PHO UBI PHO MULTI C1-INS

SA380

ELKS PRO ACT

SA381

HSP 90 PRO ACT MULTI

SA382

CDC37 PRO ACT

SA383

IKK GAMMA BR NEMO PRO ACT UBI MULTI

SA384

IKK BETA BR IKK2 PRO ACT PHO PHO MULTI

SA385

IKK ALPHA BR IKK1 PRO ACT PHO PHO PHO

SA386

MULTI
IKK BETA BR IKK2 PRO EMP EMP MULTI

SA387

IKK ALPHA BR IKK1 PRO ACT PHO PHO PHO

SA388

MULTI
IKK GAMMA BR NEMO PRO ACT UBI MULTI

SA389

ELKS PRO ACT

SA39

RIP PRO EMP UBI C1-INS

SA390

HSP 90 PRO ACT MULTI

SA391

CDC37 PRO ACT

SA392

IKK ALPHA BR IKK1 PRO EMP EMP MULTI

SA393

IKK BETA BR IKK2 PRO EMP EMP MULTI

SA394

IKK GAMMA BR NEMO PRO ACT UBI MULTI

SA395

ELKS PRO ACT

SA396

HSP 90 PRO ACT MULTI

SA397

CDC37 PRO ACT

68

SA398

P50 PRO ACT

SA399

P65/RELA PRO PHO PHO

SA4

CRD2 SIM

SA40

26S PROTEOSOME PRO ACT C1-INS

SA400

I KAPPA B ALPHA PRO PHO PHO UBI UBI

SA401

I KAPPA B BETA PRO PHO PHO UBI

SA402

P65/RELA PRO

SA403

P50 PRO

SA404

P65/RELA PRO PHO

SA405

P50 PRO ACT

SA406

CUL1 PRO ACT

SA407

SKP1 PRO ACT

SA408

P50 PRO ACT

SA409

P65/RELA PRO PHO PHO PHO

SA41

S3815 DEG C1-INS

SA410

P50 PRO ACT

SA411

P65/RELA PRO PHO PHO PHO PHO UBI

SA413

P50 PRO ACT

SA414

P65/RELA PRO PHO PHO PHO

SA415

P50 PRO ACT

SA416

P65/RELA PRO ACT PHO PHO PHO PHO UBI

SA418

P50 PRO ACT

SA419

P65/RELA PRO PHO PHO PHO UBI

SA42

A20 PRO ACT PHO C1-INS

69

SA421

APAF-1 PRO ACT

SA422

DATP SIM

SA423

CYTOCHROME C PRO ACT

SA424

PRO-A-SMASE PRO

SA425

PRE-PRO-CTSD PRO

SA426

PRE-PRO-CTSD PRO

SA427

PRO-A-SMASE PRO

SA43

A20 PRO C1-INS

SA432

BCL-XL PRO

SA433

BAD PRO ACT

SA44

CARP2 PRO C1-INS

SA443

CREB/P300 PRO EMP C2-INS

SA444

CREB/P300 PRO ACT PHO C2-INS

SA445

PKAC PRO ACT C1-INS

SA446

PKAC PRO ACT C2-INS

SA447

ATF-2 PRO C2-INS

SA448

ATF-2 PRO PHO PHO C2-INS

SA449

ATF-2 PRO ACT PHO PHO PHO C2-INS

SA45

CARP2 PRO ACT C1-INS

SA450

ELK-1 PRO C2-INS

SA451

ELK-1 PRO PHO C2-INS

SA452

ELK-1 PRO PHO PHO C2-INS

SA453

ELK-1 PRO ACT PHO PHO PHO PHO PHO C2-INS

SA454

SAP-1A PRO C2-INS

70

SA455

SAP-1A PRO ACT PHO PHO PHO PHO C2-INS

SA46

GRB-2 PRO C1-INS

SA47

GRB-2 PRO ACT C1-INS

SA470

SRE PRO ACT C2-INS

SA471

SRF PRO ACT C2-INS

SA472

C-FOS GEN C2-INS

SA473

C-FOS RNA C2-INS

SA474

SRE PRO ACT

SA475

ELK-1 PRO ACT PHO PHO PHO PHO PHO

SA476

SAP-1A PRO ACT PHO PHO PHO PHO

SA477

SRE PRO ACT

SA478

SRE PRO ACT

SA479

ELK-1 PRO ACT PHO PHO PHO PHO PHO

SA48

SOS PRO C1-INS

SA480

SRF PRO ACT

SA481

SRE PRO ACT

SA482

SAP-1A PRO ACT PHO PHO PHO PHO

SA483

SRF PRO ACT

SA484

C-FOS PRO EMP EMP C1-INS

SA485

C-FOS PRO EMP EMP C2-INS

SA486

C-FOS PRO ACT PHO PHO PHO PHO C2-INS

SA489

C-JUN PRO PHO PHO PHO PHO PHO PHO PHO PHO

SA49

C2-INS
SOS PRO ACT C1-INS

71

SA490

C-JUN PRO PHO PHO PHO EMP PHO PHO PHO PHO

SA491

C2-INS
C-JUN PRO PHO PHO PHO EMP PHO EMP PHO PHO

SA492

C2-INS
C-JUN PRO ACT PHO PHO PHO PHO C2-INS

SA493

C-JUN PRO EMP EMP EMP EMP EMP EMP EMP

SA494

EMP C2-INS
TRE PRO ACT C2-INS

SA495

C-JUN RNA C2-INS

SA496

C-JUN GEN C2-INS

SA497

TRE PRO ACT

SA498

ATF-2 PRO ACT PHO PHO PHO

SA499

C-JUN PRO ACT PHO PHO PHO PHO

SA5

STNF ALPHA PRO ACT MULTI

SA50

MADD PRO C1-INS

SA500

CK II PRO ACT C2-INS

SA501

GSK3 BETA PRO ACT EMP C1-INS

SA502

GSK3 BETA PRO PHO C1-INS

SA503

GSK3 BETA PRO ACT EMP C2-INS

SA506

XIAP GEN C2-INS

SA507

A20 GEN C2-INS

SA508

BCL2 GEN C2-INS

SA509

GADD45 BETA RNA C2-INS

SA51

MADD PRO ACT C1-INS

SA510

GADD45 BETA GEN C2-INS

72

SA511

BCL2 RNA C2-INS

SA512

XIAP RNA C2-INS

SA513

A20 RNA C2-INS

SA514

CIAP1/2 GEN C2-INS

SA515

CIAP1/2 RNA C2-INS

SA516

I KAPPA B GEN C2-INS

SA517

I KAPPA B RNA C2-INS

SA518

CYLD RNA C2-INS

SA519

CYLD GEN C2-INS

SA520

TRAF2 GEN C2-INS

SA521

TRAF2 RNA C2-INS

SA522

TRAF1 GEN C2-INS

SA523

TRAF1 RNA C2-INS

SA524

CFLIP GEN C2-INS

SA525

CFLIP RNA C2-INS

SA526

MN-SOD GEN C2-INS

SA527

MN-SOD RNA C2-INS

SA528

FHC GEN C2-INS

SA529

FHC RNA C2-INS

SA53

RAS PRO C1-INS

SA530

GADD45 BETA PRO ACT C1-INS

SA531

PTEN GEN C2-INS

SA532

PTEN RNA C2-INS

SA533

PTEN PRO ACT C1-INS

73

SA538

ITCH PRO EMP C1-INS

SA539

ITCH PRO ACT PHO PHO PHO C1-INS

SA540

C-JUN PRO EMP EMP EMP EMP EMP EMP EMP

SA541

EMP C2-INS
C-JUN PRO ACT PHO PHO PHO PHO C2-INS

SA542

C-JUN PRO EMP EMP EMP EMP EMP EMP EMP

SA543

EMP C1-INS
C-FOS PRO ACT PHO PHO PHO PHO

SA544

C-JUN PRO ACT PHO PHO PHO PHO

SA545

P53 GEN C2-INS

SA546

EGR-1 RNA C2-INS

SA547

P53 RNA C2-INS

SA548

P21 SUPER WAF1/CIP1 GEN C2-INS

SA549

P21 SUPER WAF1/CIP1 RNA C2-INS

SA55

PI3K (P85) PRO EMP C1-INS

SA550

MDM-2 PRO C1-INS

SA551

EGR-1 GEN C2-INS

SA552

CYCLIN D1 GEN C2-INS

SA553

CYCLIN D1 RNA C2-INS

SA554

MDM-2 GEN C2-INS

SA555

MDM-2 RNA C2-INS

SA558

P53 PRO C1-INS

SA559

P21 SUPER WAF1/CIP1 PRO C1-INS

SA56

RAS PRO ACT C1-INS

SA560

CYCLIN D1 PRO ACT C2-INS

74

SA561

CYCLIN D1 PRO PHO C2-INS

SA562

CYCLIN D1 PRO C1-INS

SA563

EGR-1 PRO C1-INS

SA565

P53 PRO ACT PHO C2-INS

SA566

P21 SUPER WAF1/CIP1 PRO C2-INS

SA567

P21 SUPER WAF1/CIP1 PRO ACT C2-INS

SA568

CYCLIN E PRO ACT C2-INS

SA569

CDK2 PRO ACT C2-INS

SA57

PI3K (P85) PRO ACT PHO C1-INS

SA570

G1-S PHASE TRANSITION PHE C2-INS

SA571

CELL CYCLE PHE C2-INS

SA572

CELL PROLIFERATION PHE C2-INS

SA573

MDM-2 PRO ACT

SA574

P53 PRO

SA575

CDK2 PRO ACT

SA576

CYCLIN E PRO ACT

SA577

MDM-2 PRO ACT C2-INS

SA578

P53 PRO ACT C2-INS

SA58

AKT/PKB PRO ACT PHO PHO C1-INS

SA580

CDK4 PRO ACT C2-INS

SA581

RB PRO PHO C2-INS

SA582

E2F PRO ACT C2-INS

SA583

CYCLIN E GEN C2-INS

SA584

CYCLIN E RNA C2-INS

75

SA585

CYCLIN E PRO C1-INS

SA587

CYCLIN D1 PRO ACT

SA588

CDK4 PRO ACT

SA589

RB PRO ACT

SA59

AKT/PKB PRO EMP C1-INS

SA590

E2F PRO

SA591

DP1 PRO ACT

SA594

C-MYC PRO ACT PHO PHO C2-INS

SA595

C-MYC PRO EMP PHO C2-INS

SA596

C-MYC PRO EMP EMP C2-INS

SA597

IL-6 GEN C2-INS

SA598

IL-8 GEN C2-INS

SA599

CCL-2 GEN C2-INS

SA6

NSMASE PRO C1-OUT

SA60

CAPP PRO C1-INS

SA600

CCL-2 RNA C2-INS

SA601

IL-8 RNA C2-INS

SA602

IL-6 RNA C2-INS

SA603

CCL-2 PRO C1-INS

SA604

IL-6 PRO ACT C1-INS

SA605

IL-8 PRO ACT C1-INS

SA606

EGR-1 PRO ACT C2-INS

SA607

CCL-2 PRO ACT C2-INS

SA608

IL-6 PRO ACT C2-INS

76

SA609

IL-8 PRO ACT C2-INS

SA61

CAPP PRO ACT C1-INS

SA611

MKPS GEN C2-INS

SA612

MKPS RNA C2-INS

SA614

JNK 1 PRO EMP C2-INS

SA615

MKPS PRO ACT C2-INS

SA616

MKPS PRO ACT C1-INS

SA62

VAV PRO C1-INS

SA63

VAV PRO ACT PHO C1-INS

SA64

PAK 3 PRO C1-INS

SA65

PAK 3 PRO ACT PHO C1-INS

SA660

SPHK1 PRO C1-INS

SA661

SPHK1 PRO ACT C1-INS

SA662

SPHK1 PRO ACT PHO C1-INS

SA663

SPHK1 PRO ACT PHO C1-INS

SA665

SPHINGOSINE PRO C1-INS

SA667

SPHINGOSINE PRO ACT PHO C1-INS

SA672

S4560 DEG C1-INS

SA673

S4561 DEG C1-INS

SA676

PTEN PRO ACT C2-INS

SA677

BCL-2 PRO ACT C2-INS

SA68

RAC/CDC42 PRO ACT C1-INS

SA688

BCL-2 PRO ACT C5-INS

SA69

RAC/CDC42 PRO C1-INS

77

SA7

NSMASE PRO ACT C1-INS

SA70

GCK PRO C1-INS

SA700

BCL-XL PRO ACT C5-INS

SA701

RIPK3 PRO ACT C1-INS

SA703

CREB/P300 PRO ACT PHO

SA704

CREB/P300 PRO ACT PHO

SA705

CREB/P300 PRO ACT PHO

SA71

GCK PRO ACT C1-INS

SA72

MEKK1 PRO EMP EMP C1-INS

SA73

MEKK1 PRO PHO PHO C1-INS

SA74

TAK1 PRO C1-INS

SA75

MEKK3 PRO C1-INS

SA76

MEKK3 PRO ACT PHO C1-INS

SA77

TAK1 PRO ACT PHO PHO PHO C1-INS

SA78

S4075 DEG C1-INS

SA8

FAN PRO ACT C1-INN

SA80

NIK PRO EMP C1-INS

SA81

NIK PRO EMP PHO PHO PHO C1-INS

SA84

NIK PRO ACT PHO C1-INS

SA85

MKK6 (MAPKK6 COMMA BR MEK6 COMMA

SAPKK3 ) PRO C1-INS

SA86

MKK7 BR (JNKK2) PRO C1-INS

SA87

MKK3 (MEK3 COMMA BR MAPKK3) PRO C1-INS

SA88

MKK4/JNKK1/SEK1 PRO EMP C1-INS

78

SA89

MKK6 (MAPKK6 COMMA BR MEK6 COMMA

SAPKK3 ) PRO ACT PHO PHO C1-INS

SA9

FAN PRO C1-OUT

SA90

MKK7 BR (JNKK2) PRO ACT PHO PHO C1-INS

SA91

MKK3 (MEK3 COMMA BR MAPKK3) PRO ACT PHO

SA92

PHO C1-INS
MKK4/JNKK1/SEK1 PRO ACT PHO C1-INS

SA93

CRAF/RAF-1 PRO C1-INS

SA94

B-RAF PRO C1-INS

SA96

PKC ALPHA PRO C1-INS

SA97

PKC ALPHA PRO ACT PHO PHO PHO PHO C1-INS

SA98

TRX PRO ACT C1-INS

SA99

ASK1 PRO C1-INS

79