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Network Graph
1 2 3 4 5 6
8.1
2.5
Vertex-Weighted Edge-Weighted
Networks As Graphs - 2
A network can be connected (presented by a single component) or
disconnected (presented by several disjoint components).
connected disconnected
Networks having no cycles are termed trees. The more cycles the
network has, the more complex it is.
trees
cyclic graphs
Networks As Graphs - 3
Some Basic Types of Graphs
Paths
Stars
Cycles
Complete Graphs
Bipartite Graphs
Air Transportation Network
The World Wide Web
Fragment of a Social Network
(Melburn, 2004)
Biological Networks
A. Intra-Cellular Networks
Protein interaction networks
Metabolic Networks
Signaling Networks
Gene Regulatory Networks
Composite networks
Networks of Modules, Functional Networks
Disease networks
B. Inter-Cellular Networks
Neural Networks
D. Ecological Networks
E. Evolution Network
GENOME
miRNA
_____________________ regulation?
-
- protein-gene
interactions
PROTEOME
protein-protein
interactions
METABOLISM
Bio-chemical
reactions
Citrate Cycle
The Protein Network of Drosophila
Metabolic Networks
Apoptosis Pathway - 1
Apoptosis is a mechanism of controlled cell death
critically important in many biological processes
Cleavage of Caspase
CASP6 Substrates
DISC
CASP10
Heterodimer DFF
Membrane
Death protein DFF45 DFF40
CASP8
activator
381 organisms
Functional Networks
Yeast: 1400 proteins, 232 complexes, nine functional groups of complexes
Cell Cycle Cell Polarity & Structure
13 7 8 Number of protein complexes
111 25 40 61 Number of proteins
Transcription/DNA
77 15 19 Number of shared proteins
Maintenance/Chromatin 14 11
Structure 30 16 27 7 22 Intermediate
55 187 43
740 94 33 221 and Energy
73 Metabolism
83 37 103
65
Signaling 11
20 13 20 Membrane
125 53 147 Biogenesis &
Turnover
35
41 321 19 299 49
97 75
5
RNA 28 9 33 Protein Synthesis
24 260
Metabolism 692 6 419 and Turnover
172 12 75
160
Protein RNA / Transport
All Complex Dynamic Networks
Have Similar Structure and
Common Properties
Hubs
Scale-Freeness
Small-Worldness
Centrality
Robustness/Fragility
How To Characterize
a Network?
Quantifying Networks
A. Graph-Theoretical (Topological) Descriptors
A1. Connectivity-based:
A2. Distance-based
B. Information-Theoretic Descriptors
B1, Compositional
B2. Structural
C. Complexity Measures
C1. Subgraph Count
C2. Overall Connectivity
C3. Walk Count
C4. Small-World Connectivity
Connectivity-Based Topological
Descriptors
Adjacency Matrix
1 2 3 4 5 ai
1
1 0 0 1 0 0 1
2 0 0 1 0 0 1
A(G) = 3 1 1 0 1 0 3
4 0 0 1 0 1 2
1 3 2 1
node degrees
5 0 0 0 1 0 1
ai – node degree
Connectivity Descriptors
Local (node) descriptors: vertex (node) degrees, ai
V
ai aij j neighborsaij
j 1
V V V
A(G) ai aij
i 1 i 1 j 1
Connectivity Descriptors-2
Average and Normalized Descriptors
ai A(G) / V
In-degree = -1 Out-degree = +1
1 2 3 4 5 ai(out)
2 3 4 5 1 0 0 1 0 0 +1
2 0 0 1 0 0 +1
A(DG) = 3 1 0 0 0 0 +1
-1,1 4 0 0 1 0 0 +1
5 0 0 0 1 0 +1
ai(in) -1 0 -3 -1 0
1 1 2 3 4 5 di 6 7
1 0 2 1 2 3 8
D(G) =
2 2 0 1 2 3 8 2 3
3 1 1 0 1 2 5 4
2 3 4 5 4 2 2 1 0 1 6
5 3 3 2 1 0 9
5
node distance, di d i d ij
j 1
Network descriptors:
V V V
d i D(G) / V
Average network distance, <d>
(average degree of separation, average path length)
d D / V (V 1)
Example
8 D = 8+8+5+6+9 = 36
d
Adjusted Average Network Distance AD( DG )
Acc
Example: 9 9
8
7 1 0
6 8 12
G DG
9 9
D = 52, <d(G)> = 52/(6x5) = 1.73 D = 34, <d(DG)> = 34/20 = 1.70 < D(G)??
The more diverse the distribution of system elements, the larger its
information content.
The more complex the system, the larger its information content.
where pi = Ni / N, and Σ pi = 1.
k
Mean Information: I ( ) p i log 2 p i , bits/element
i 1
k
Total Information: I tot ( ) N log N N i log N i , bits
i 1
2
degrees 4
mI(deg) = -(4/14)log2(4/14) –(3/14)log2(3/14) –
3x(2/14)log2(2/14) – (1/14)log2(1/14) = 2.47 bits/node
3
2 1
mI
A = 14 tot(deg) = 14log214 – 4log24 – 3log23 -3x2log22 -1log21 = 34.55 bits
2
mI
norm(deg) = 34.55/(14log214) = 0.648
9
distances mI(deg) = -(12/52)log2(12/52) – 2x(9/52)log2(9/52) –
2x(8/52)log2(8/52) – (6/52)log2(6/52) = 2.55 bits/node
8
6 8 12 mI(dist) = 52log252–12log212–2x9log29–2x8log28-6log26 = 132.83 bits
9 D = 52
mI
norm(deg) = 132.83/(52log252) = 0.448
Network Complexity Descriptors - 1
Subgraph Count, eSC
Overall Connectivity, eOC
1
Example V = 5, E = 4 e = number of edges
1 3 2 1
Example
1 3 4 5
1 2
SC 28(5,8,9,5,1) 30(5,9,10,5,1)
WC 15(5,5,5) 21(5,7,9)
Can one unite the two patterns into a single complexity measure?
A V
ai V
B1 B2 bi
D i 1 d i i 1
6
3 4 5
SC = 11 17 20 26
OC = 32 76 100 160
WC = 58 106 140 150
B1 = 0.2 0.222 0.250 0.333
B2 = 1.105 1.294 1.571 1.6667
7 9
8 10
SC = 29 31 54 57
OC = 190 212 482 522
WC = 178 214 300 350
B1 = 0.313 0.313 0.429 0.400
B2 = 1.6774 1.783 2.200 2.211
11 13 14 15
12
SC = 61 114 119 477 973
OC = 566 1316 1396 7806 18180
WC = 337 538 638 1200 1700
A/D = 0.429 0.538 0.538 0.818 1
B2 = 2.410 2.867 2.943 4.200 5