Network

Nodes

Edges

Enumeration of cycles

Enumeration of inputoutput paths


  
Number of cycles

EMC

Johnson

Number of I/O paths

EMC

Breadthfirst

   
[s]

[s]
 
[s]

[s]

Tcell

94

138

100

0.1

0.04

8058

0.98

0.27

EGFR

106

230

237

0.15

0.07

384766

131

21

Tcell+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 graphalgorithms (Johnson's algorithm and breadthfirst search, respectively). The number of edges refers to unique edges (parallel edges with the same sign and halfedges are removed before calculation). The values for the combined network "Tcell+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.