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This journal is c The Royal Society of Chemistry 2011 Mol. BioSyst., 2011, 7, 1263–1269 1263
Cite this: Mol. BioSyst., 2011, 7, 1263–1269
Resilience of protein–protein interaction networks as determined by their
large-scale topological featuresw
Francisco A. Rodrigues,*aLuciano da Fontoura Costa
band Andre Luiz Barbieri
b
Received 1st November 2010, Accepted 7th January 2011
DOI: 10.1039/c0mb00256a
The relationship between the structure and function of biological networks constitutes a
fundamental issue in systems biology. Particularly, the structure of protein–protein interaction
networks is related to important biological functions. In this work, we investigated how such a
resilience is determined by the large scale features of the respective networks. Four species are
taken into account, namely yeast Saccharomyces cerevisiae, worm Caenorhabditis elegans, fly
Drosophila melanogaster and Homo sapiens. We adopted two entropy-related measurements
(degree entropy and dynamic entropy) in order to quantify the overall degree of robustness of
these networks. We verified that while they exhibit similar structural variations under random
node removal, they differ significantly when subjected to intentional attacks (hub removal). As a
matter of fact, more complex species tended to exhibit more robust networks. More specifically,
we quantified how six important measurements of the networks topology (namely clustering
coefficient, average degree of neighbors, average shortest path length, diameter, assortativity
coefficient, and slope of the power law degree distribution) correlated with the two entropy
measurements. Our results revealed that the fraction of hubs and the average neighbor degree
contribute significantly for the resilience of networks. In addition, the topological analysis of the
removed hubs indicated that the presence of alternative paths between the proteins connected to
hubs tend to reinforce resilience. The performed analysis helps to understand how resilience is
underlain in networks and can be applied to the development of protein network models.
Introduction
The study of molecular biology has received much inter-
disciplinary attention focused on complex interactions in
biological systems, which has led to a new perspective, i.e.
holism instead of reduction.1 Biological processes depend on
the interaction between proteins as well as between proteins
and other molecules,1 which generate networks of interactions.
Though protein–protein interaction networks have been
studied for a long time (e.g. ref. 2), only recently graph
theoretical concepts and measurements were applied for
respective analysis (e.g. ref. 3). Proteins can interact in order
to form a cellular complex, where each protein can carry
another protein, or interact briefly with a target protein in
order to modify it. Protein interaction maps can be naturally
represented as networks, where the nodes represent proteins
and the edges represent interactions.4
One particularly important object of investigation by
systems biology researchers has been the relationship between
the structure of biological networks and their respective func-
tions that control the information flow and regulation of
cellular signals.5,6 Indeed, it has been verified that the structure
of protein–protein interaction networks differs from random
networks of the type Erdos and Renyi models,7 but presents a
structured organization that follows the scale-free paradigm,8
characterized by the fact that the distribution of the number of
connections follows a power law. Actually, the distribution of
connections of protein–protein interaction networks follow a
power law with a cutoff exponential.9,10 This type of topology
is particularly interesting because it accounts for the existence
of hubs, i.e. nodes with particularly high degrees, which are
known to play an important role in networks.11 As a matter of
fact, hubs have an intrinsic relationship with lethality, as
verified in recent works (e.g. ref. 9 and 12).
The investigation of the relationship between the network
organization and function can be performed by gene deletion.
In recent experiments, the analysis of robustness of biological
networks was performed experimentally by studies in a direct
response to gene deletions13 or RNA interference.14 These
aDepartamento de Matematica Aplicada e Estatıstica, Instituto deCiencias Matematicas e de Computacao, Universidade de SaoPaulo-Campus de Sao Carlos, Caixa Postal 668, 13560-970Sao Carlos, SP, Brazil. E-mail: [email protected]
b Instituto de Fsica de Sao Carlos, Universidade de Sao Paulo,Av. Trabalhador Sao Carlense 400, Caixa Postal 369CEP 13560-970, Sao Carlos, Sao Paulo, Brazil
w Electronic supplementary information (ESI) available. See DOI:10.1039/c0mb00256a
MolecularBioSystems
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1264 Mol. BioSyst., 2011, 7, 1263–1269 This journal is c The Royal Society of Chemistry 2011
experiments are fundamental approaches to understanding the
global organization of gene functions.13 Computationally, the
examination of perturbations can be implemented by random
or preferential removal of proteins in protein interaction
networks.15 In the former case, all proteins have the same
probability to be removed, while in the latter, proteins are
selected according to a given attribute, such as the respective
number of connections. A previous work analyzed the
robustness of proteins of the Saccharomyces cerevisiae,
Caenorhabditis elegans and Drosophila melanogaster, where
the authors described the variation of network diameter under
fails, i.e. random removal, and attacks, achieved by deleting
the most connected proteins while following the order of their
number of connections.16 However, that work provided only a
partial picture of network resilience since it did not provide
any explanation about which topological feature is contributing
to the network’s robustness. In addition, only one particular
network property, i.e. the diameter, was analyzed. In fact,
since the organization of the networks is a product of natural
selection, it is expected that the structure of biological networks
of different species should differ in some way. Here, we present
a quantification of how several important structural properties
contribute for the resilience of protein–protein interaction
networks.
In order to verify this relationship between resilience and
network organization, we performed a comparative analysis
of different species calculating the entropy of connectivity
distribution17 and the dynamics entropy based on the Markov
process,18 which are robustness-related measurements. Parti-
cularly, the dynamical entropy for a Markov process was
applied recently in the analysis of a protein network of the
yeast S. cerevisiae,19 revealing that proteins with large
contribution to network entropy are frequently lethal. These
adopted measurements proved to be consistent with our
performed simulations. The relationship between the structure
and function of networks can be quantified in terms of the
correlation between these entropy-based measurements and
network topological features. In fact, this analysis can reveal
which structural property of networks is more determinant for
network resilience. We verified that two topological features
appear to contribute particularly for this resilience, namely
the coefficient of the power law degree distribution and the
average neighbor degree. In addition, we verified that the
networks of the S. cerevisiae, C. elegans, D. melanogaster
and Homo sapiens present similar behavior when subjected
to random fails. This result agrees with the experimental
observation, where a large number of perturbations did not
result in any phenotypic perturbation variation under a given
experimental condition.13,14 On the other hand, their networks
topologies have a different behavior under intentional attacks.
As a matter of fact, the networks of H. sapiens and
D. melanogaster revealed to be more robust under intentional
attacks than the networks of S. cerevisiae and C. elegans.
Therefore, the more complex an organism is, the higher is its
resilience to attacks. Since we identified which features are
mainly responsible for increased network resilience, these
results help to understand the organization and function of
protein interactions, and can be applied in the development of
more precise protein–protein interaction network models.
In next sections, we present methodologies for description
of network topology and quantification of network resilience.
The results and discussion are presented subsequently,
followed by a description of the simulations considering
random fails and intentional attacks.
Protein–protein interaction databases
In order to compare networks of different species, we
considered two databases from different sources for each
species. This adoption paved the way to a more reliable
comparison, since the adopted databases provided networks
with different number of proteins and connections (i.e. different
levels of completeness). For the yeast S. cerevisiae, we adopted
the database of the Center for Cancer Systems Biology
(CCSB), which provides high-quality binary interaction
information.20 This database is considered a ‘‘second-generation’’
high-quality high-throughput Y2H dataset covering about
20% of all yeast binary interactions.20 This database covers
1809 interactions among 1278 proteins (we name this network
as Sce-CCSB). The second database is based on Ito-core and
Uetz-screens and is composed by 2930 interactions among
2018 proteins (here named Sce-Union).21 In the case of the
worm C. elegans, we took into account two databases: (i) the
Worm Interactome,22 from the CCSB (named Cel-Wi), which
is composed by 1496 proteins and 1816 interactions (from
Vital Lab 2007), and (ii) the worm database by the Biogrid,23
version 3.0.65 (named Cel-BG), composed by 3518 proteins
and 6672 interactions. The databases of D. melanogaster
were also obtained from the Biogrid,23 version 3.0.65 (named
Dme-BG), formed by 7282 nodes and 27 671 connections; and
from the Drosophila Interaction Database (DroiD), which
includes protein interaction data generated in the Finley
laboratory using the LexA yeast two-hybrid system, mostly
from high throughput screens.24 This latter database resulted
in a network (named Dme-FI) composed by 1338 nodes and
3161 interactions. At last, for the H. sapiens, we took into
account the database by Biogrid,23 also version 3.0.65 (named
Hsa-BG), composed by 9527 proteins and 36 877 interactions;
and the Human Protein Reference Database release 9,25
formed by 9612 proteins and 39 128 interactions (named
Has-HPRD). For all these databases, only the largest compo-
nent was taken into account while performing the resilience
analysis.
Methods
Topological measurements
Protein–protein interaction networks are types of undirected
complex networks formed by a set of N nodes (or vertices)
connected by E edges. A network can be represented by its
adjacency matrix A, whose elements aij and aji are equal to one
whenever there is a connection between the proteins i and j,
and equal to zero otherwise. The topology of protein–protein
interaction networks can be described by a set of network
measurements,26 which can quantify the network connectivity,
presence of cycles and distances between a pair of nodes.
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The degree of a protein i, hence ki, is equal to the number of
edges connected to that protein and can be calculated as
ki ¼X
j
aij ¼X
j
aji: ð1Þ
The average degree of a network is the average of ki for all
vertices in the network,
hki ¼ 1
N
X
i
ki ¼1
N
X
ij
aij : ð2Þ
The average degree quantifies the density of connections. The
degree distribution P(k) yields the probability of finding a
node with degree k in a network.
Protein–protein interaction networks present cycles of order
three, given by triples of three connected vertices. One way to
characterize the presence of loops of this order is through the
clustering coefficient. The clustering coefficient cc of a protein i
is defined as the number of links li between the nodes within its
neighborhood divided by the number of edges that could
possibly exist between them (ki(ki � 1)/2).
The average neighbor connectivity, r(i), measures the average
degree of the neighbors of each vertex i in the network.27 This
amount is calculated by finding the neighbors of given proteins
and averaging their connectivities. The global respective
measurement is given by averaging the neighbor degrees for
all vertices, represented by r.
The average shortest path length (sp) is calculated by taking
into account the shortest distance between each pair of vertices
in the network. The diameter of a network corresponds to the
longest length among all shortest paths.
The assortative coefficient, henceforth s, measures the
correlation between vertex degrees.28 More specifically, it is
obtained by calculating the Pearson correlation coefficient
between the degrees of each pair of nodes. If s > 0 the
network is assortative; if s o 0, the network is disassortative;
for s = 0 there are no correlations between vertex degrees.
While in assortative networks nodes with a similar degree tend
to connect to each other, in disassortative structures the highly
connected nodes tend to be attached to poorly connected
nodes.28
Resilience-related measurements
The resilience of protein networks can be quantified by
entropy related measurements.17,19 The entropy of the degree
distribution has revealed to be an effective measure of net-
work’s resilience under perturbations.17 This measurement
provides an average measure of the network’s heterogeneity,
since it measures the diversity of the link distribution. The
entropy of the degree distribution P(k) can be defined as
follows:
H ¼ �X
k
PðkÞ log½PðkÞ�: ð3Þ
In the case of protein–protein interaction networks, which
present a power-law degree distribution with an exponential
cutoff, as the scaling exponent g increases, the network
becomes less heterogeneous and, as a result, a lower entropy
value should be observed.
The other adopted resilience-related measurement is the
dynamic entropy, which is based on stochastic dynamic of
random walks. This particular dynamic has been used for
modeling of sequential protein activations, such as signal
transduction,29 as described in ref. 12. The dynamical entropy
of a Markov process characterizes the diversity of possible
pathways and is related to the response of the system to
perturbations.30 This measurement was used for characteriza-
tion of proteins in the networks of the yeast, revealing that
proteins with large contribution to network entropy are
preferentially lethal.19 The dynamical entropy is calculated
by the following equation:18
Hd ¼ �X
ij
pipij logðpijÞ; ð4Þ
where pij was obtained from the transition probability matrix,
whose elements pi,j = ai,j/kj. That is, each element pij repre-
sents the probability of movement of a random walker from
node i to node j in one step. The term pi represents the
components of the stationary distribution, i.e. p is defined as
the left-hand eigenvector associated with the largest eigenvalue
1 of the stochastic matrix P, pP = p. Since the entropy of
the degree distribution and the dynamical entropy are well-
established measurements,17,19 we used both in the quantifi-
cation of network resilience.
Discussion
The large scale organization of protein–protein interaction
networks
The cumulative degree distribution for all protein–protein
interaction networks follows a power law with an exponential
cut-off, which is due to the finite size effect,31 described by
P(k) C kge�k/kc (5)
Fig. 1 shows the cumulative distribution (Pcum(k) =RN
k
P(x)dx) obtained for all eight networks. The values of g,
Fig. 1 Cumulative degree distribution of the protein–protein inter-
action networks of S. cerevisiae (Sce-CCSB and Sce-Union), C. elegans
(Cel-Wi and Cel-BG), D. melanogaster (Dme-BG and Dme-Fl) and
H. sapiens (Hsa-BG and Hsa-CCSB).
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obtained by using the least squares method, are shown in
Table 1.
The clustering coefficient resulted relatively small for all
networks, indicating that two connected proteins tend not to
share the same set of neighbors. In addition, the small values
of the average shortest path length indicate that all considered
protein networks are small-world, which can be a consequence
of the presence of hubs. It is interesting to note that smaller sp
values tended to be obtained for more complex species. In fact,
the smaller the shortest path, the faster the communication
between nodes, an aspect that can be related to resilience.32
The diameter of the networks seems to be preserved for all
species, varying from 12 to 16. The average neighbor degree
also is likely to be higher for more complex species, with the
H. sapiens and D. melanogaster presenting the highest values.
All investigated protein networks are disassortative, exhibiting
smaller coefficient s for the yeast and worm. Similar behavior
was observed for the coefficient of the degree distribution.
Actually, the protein interaction networks of S. cerevisiae and
C. elegans have the lowest degree exponent g, which means
that the topologies of these networks are mostly dominated by
the highly connected proteins. In next sections, we verify that
this property seems to be fundamental for defining the level of
network resilience.
Random fail
We start our dynamic analysis by investigating the effect of
random removal of proteins from the networks of the four
considered species. This task was achieved without any
preferential rule, i.e. all proteins had the same probability to
be selected for removal in a network. Fig. 2 presents the
variation of the size of the largest component, diameter and
average shortest path for each network. These measurements
are those most frequently adopted in the literature for analysis
of resilience (e.g. ref. 11), since they quantify the network’s
ability to keep its normal behavior under external or internal
perturbations. Note that each network measurement was
normalized with respect to its original value, i.e. the measure-
ment calculated from the network without perturbations. This
approach was adopted since networks present different num-
ber of vertices and edges. Moreover, the studied measurements
depend on the networks size and density of connections.
Therefore, the normalization allowed us to investigate only
the variation of the measurement while avoiding effects
imposed by the network size and connection density. In
Fig. 2, it can be observed that all networks presented similar
behavior. The main difference occurred for the largest compo-
nent of the S. cerevisiae and C. elegans. Furthermore, the
diameter and the average shortest path of all networks present
very small variations. Therefore, the networks of all species
exhibit similar resilience against random fails, not mattering
the complexity of the organism. Indeed, this is a consequence
of the fact that all these networks are scale-free presenting
degree distribution that follows a power-law with an expo-
nential cutoff, as shown in Fig. 1. These obtained results
corroborate experimental observations, which showed that a
large number of perturbations does not result in any pheno-
typic perturbation variation under a given experimental
condition.13,14
Table 1 Set of measurements obtained from the networks of the four considered species: average clustering coefficient (cc), average shortest pathlength (sp), network diameter (d), average neighbor connectivity (r), assortative coefficient (s), the scaling exponent of the power law (g)
Species cc sp d r s g H Hd
S. cerevisiae (Sce-CCSB) 0.056 5.35 14 3.08 �0.16 �2.47 2.56 2.47S. cerevisiae (Sce-Union) 0.057 5.61 14 3.06 �0.11 �2.47 2.59 2.41C. elegans (Cel-Wi) 0.017 5.72 16 2.71 �0.25 �2.53 2.20 2.37C. elegans (Cel-BG) 0.060 4.32 13 3.85 �0.17 �2.17 2.55 3.50D. melanogaster (Dme-BG) 0.046 4.32 11 6.93 �0.04 �1.77 3.88 3.79D. melanogaster (Dme-Fl) 0.043 4.50 12 5.02 �0.15 �2.05 3.09 3.53H. sapiens (Hsa-BG) 0.157 4.48 14 6.76 �0.07 �1.96 3.79 3.86H. sapiens (Hsa-CCSB) 0.106 4.21 14 8.00 �0.04 �1.91 4.09 4.11
Fig. 2 Random fails in protein–protein interaction networks. The variation of the size of largest component (a), diameter (b) and average shortest
path length (c) as a function of the fraction of removed vertices for the protein–protein interaction networks of S. cerevisiae (Sce-CCSB and
Sce-Union), C. elegans (Cel-Wi and Cel-BG), D. melanogaster (Dme-BG and Dme-Fl) and H. sapiens (Hsa-BG and Hsa-CCSB). Each point is an
average over 1000 simulations. The lines are only guides for the eye.
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Intentional attack
The resilience of protein–protein interaction networks was
also investigated with respect to intentional attacks. In this
case, the most connected nodes were removed sequentially,
according to their degree, and a respective measurement was
calculated. We performed such analysis removing upto 5% of
the total number of vertices and obtained the relative variation
of the giant component, network diameter and average shortest
path length. As done in the case of random fails, the relative
variation was obtained by the ratio between the measurement
calculated when a fraction f of nodes was removed and the
original measurement. Fig. 3 presents the obtained results.
Different from the random fails, the structural variation of the
networks under attacks depends on the organism complexity.
In all cases, the more complex an organism, the more resilient
it tends to be to intentional attacks. The protein–protein
interactions of the D. melanogaster and H. sapiens are the
most robust, while the network of the S. cerevisiae is the least
resilient. In the next section, we investigate which topological
properties are mainly responsible for protein network
robustness.
Relationship between network structure and resilience
Entropy-related measurements, namely the structural17 and
dynamic entropy,19 have been taken into account for quanti-
fication of network robustness in networks. We adopted these
measurements in order to identify which properties of net-
works contribute more decisively for the resilience of the
protein–protein interaction networks. Table 1 presents the
obtained entropy values for each network. Comparing these
values with the curves in Fig. 2 and 3, we can observe a good
agreement between them, i.e. more resilient networks tend to
have higher dynamic and structural entropies. In this way, we
considered a set of six measurements and calculated their
Pearson correlation coefficient with the entropy of connectiv-
ity distribution and the dynamics entropy. This approach
allowed the identification of clear relationships between each
given structural features and the overall network robustness.
Fig. 4 presents the obtained relationships between the dynamic
entropy and the adopted measurements. The correlations
between the entropy of the degree distribution and each
measurement (r), as well as between the dynamic entropy
and each network measurement, are also given in this figure.
By comparing the correlation values, it can be observed that
the average neighbor degree, r, and the coefficient of power
law, g, are the measurements that present the highest correla-
tions with the entropies. These two properties are potentially
contributing in a particularly strong way for the resilience
altogether. In order to verify the difference between the
average neighbor degrees of all considered species, we
calculated the distributions of these measurements by taking
into account only the removed hubs, which represent 5% of
the total number of proteins. Fig. 5 shows the obtained results.
The median values for each distribution are also indicated in
this figure. We took into account the median instead
of the mean because the distributions are not symmetric.33
It can be observed that H. sapiens and D. melanogaster exhibit
hubs with larger average neighbor degree than the S. cerevisiae
and the C. elegans. Therefore, our results suggest that
this mechanism of reinforcing the connections of the
neighbors of hubs is particularly accountable for the higher
resilience of more evolved organisms. Indeed, large values of
average neighbor degree of hubs indicate alternative connec-
tions between neighbors of such nodes, which favor the
network resilience. As a result, the high density of connections
between nodes connected to hubs tends to minimize the hub
removals.
Although the average neighbor degree and the coefficient of
power law presented the highest correlation with the entropy
coefficients, the other measurements also exhibit a significant
correlation. The shortest path length is strongly correlated,
negatively, with the dynamic entropy, indicating that small
shortest path lengths favor resilience. In fact, the high density
of connections among the neighbors of each node tends to
create alternative paths between pairs of nodes reducing the
network average shortest path length. The network diameter
presents a smaller correlation with the entropy measurements
than the average shortest path length. It is interesting to note
that the assortativity coefficients are not strongly correlated
with the resilience related measurements, indicating that this
feature is not contributing significantly for the resilience. In
fact, the smaller is this coefficient, the less robust the network.
This result corroborated other works, which verified that the
Fig. 3 Intentional attacks in protein–protein interaction networks. The variation of the size of largest component (a), diameter (b) and average
shortest path length (c) as a function of the fraction of removed vertices for the protein–protein interaction networks of S. cerevisiae (Sce-CCSB
and Sce-Union), C. elegans (Cel-Wi and Cel-BG), D. melanogaster (Dme-BG and Dme-Fl) andH. sapiens (Hsa-BG and Hsa-CCSB). Each point is
an average over 1000 simulations. The lines are only guides for the eye.
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assortative network is considerably more robust against the
removal of vertices than the disassortative networks.28
Conclusion
The relationship between the structure and dynamics is a
fundamental issue in complex networks theory. In order to
investigate the behavior of protein–protein interaction
networks under random fails and intentional attacks, we
compared eight networks, corresponding to four species,
namely the yeast S. cerevisiae, the worm C. elegans, the fly
D. melanogaster and the H. sapiens. Computer simulations
revealed that the diameter, shortest path length and size of the
giant component have similar variations in all species when
their respective networks are subjected to random removal of
proteins. These results are in agreement with previous experi-
mental observations, which showed that a large number of
perturbations does not result in any phenotypic perturbation
variation under a given experimental condition.13,14 On the
other hand, these networks revealed different topological
variations when subjected to intentional attacks. As a matter
of fact, the networks of H. sapiens and D. melanogaster
are more robust under hubs removal than the networks of
S. cerevisiae and C. elegans. Thus, more complex species tend
to have higher resilience against intentional attacks in the
respective network.
The relationship between resilience and network organiza-
tion was analyzed by taking into account robustness related
measurements—namely the entropy of the degree distribution
and the dynamics entropy based on the Markov process—and
topological measurements. We calculated the correlation
between six structural measurements and these entropy-related
quantities. We verified that two topological features contri-
buted significantly for the resilience, namely the density of
hubs, quantified by the coefficient of the power law degree
distribution, and the average neighbor degree. Particularly, the
analysis of the distribution of the average neighbor degree of
the removed hubs for all species shows that these measure-
ments are higher for more complex species. This indicates that
the presence of alternative paths between the proteins
Fig. 4 The obtained correlations between the entropy of the degree distribution and each measurement are indicated by r. The points in black are
related to the dynamic entropy Hd, and those in gray to the entropy of the degree distribution H. The structural measurements are the average
clustering coefficient cc, the average shortest path length sp, the network diameter d, the average neighbor degree r, the assortativity coefficient s
and the scale coefficient of the power law degree distribution, g. P-values for testing the hypothesis of no correlation against the alternative that
there is a nonzero correlation are indicated by the numbers in brackets.
Fig. 5 Distribution of the average neighbor degree for the removed
hubs of S. cerevisiae (Sce-CCSB and Sce-Union), C. elegans (Cel-Wi
and Cel-BG), D. melanogaster (Dme-BG and Dme-Fl) and H. sapiens
(Hsa-BG and Hsa-CCSB). The median of each distribution, m, is also
indicated in the respective plots.
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This journal is c The Royal Society of Chemistry 2011 Mol. BioSyst., 2011, 7, 1263–1269 1269
connected to hubs reinforces the resilience. The remaining four
studied measurements also contributed for resilience, but less
decisively.
The results presented in the current paper are fundamental for
the understanding of the relationship between the large scale
organization of protein–protein interaction networks and the
respective biological functions. The particularly investigated role,
i.e. the resilience, is related to biological evolution and organism
organization.34 Thus, the identification of which role is favoring
the evolution can help the development of computational models
of protein network evolution, such as ref. 35, and understand
which mechanisms are used during the natural evolution to
produce robust architectures. Further investigation can be
performed by taking into account other network topological
measurements and other removal dynamics, such as considering
the deletion of nodes belonging to a given class of proteins. Edges
removal can also be investigated by a similar approach. Other
measurements for quantification of the resilience of protein
interaction networks can also be developed. The application of
resilience analysis with respect to metabolic and transcriptional
regulatory networks constitutes another promising investigation.
Acknowledgements
Luciano da F. Costa thanks CNPq (301303/06-1) and FAPESP
(05/00587-5) for sponsorship. Andre L. Barbieri thanks CAPES
for the financial support.
References
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