|
Network
|
Nodes
|
Edges
|
Enumeration of cycles
|
Enumeration of input-output paths
|
|---|
| | | |
Number of cycles
|
EMC
|
Johnson
|
Number of I/O paths
|
EMC
|
Breadth-first
|
| | | | |
[s]
|
[s]
| |
[s]
|
[s]
|
|
T-cell
|
94
|
138
|
100
|
0.1
|
0.04
|
8058
|
0.98
|
0.27
|
|
EGFR
|
106
|
230
|
237
|
0.15
|
0.07
|
384766
|
131
|
21
|
|
T-cell+EGFR
|
200
|
410
|
337
|
6.0 ± 0.9
|
0.14 ± 0.01
|
n/a
|
n/a
|
n/a
|
|
Regulon DB
|
1493
|
3565
|
132
|
194
|
0.77
|
44194
|
4716
|
38
|
|
CA1 neuron
|
512
|
1047
|
n/a
|
n/a
|
n/a
|
n/a
|
n/a
|
n/a
|
|
Cancer signaling
|
1240
|
3144
|
n/a
|
n/a
|
n/a
|
n/a
|
n/a
|
n/a
|
- The running times when using elementary modes computation (columns "EMC") are compared with those of the graph-algorithms (Johnson's algorithm and breadth-first search, respectively). The number of edges refers to unique edges (parallel edges with the same sign and half-edges are removed before calculation). The values for the combined network "T-cell+EGFR" are mean and standard error over ten runs with different random connections between the two networks. An entry n/a indicates that the procedure quickly ran out of memory (3 GB) because of a combinatorial explosion of paths or cycles. The platform used was MATLAB 2006 b under 32 bit Linux with an Intel E6600 processor.
