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Table 2 Consistency check, results and time performance

From: BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks

Network

Interactions

Nodes

Edges

Dataset size

BioQuali

COMA

     

Results

Time

Results

Time

E. coli[14]

TF-gene

1499

3250

-

1 GI

21s.

-

-

E. coli[14]

[TF|Sigma]-gene

1916

5140

-

Cons.

21s.

-

-

E. coli[14]

[TF|Sigma]-gene

1916

5142

45 [14]

498 Pred.

30s.

10 LI

≤ 1s

E. coli[14]

[TF|Sigma]-gene

1916

5142

255 [24]

16 GI

420s.

14 LI

≤ 1s

Corynebacterium[15]

Protein-DNA

573

806

65 [26]

123 Pred.

20s.

5 LI

≤ 1s.

  1. This table summarizes the results and time performance (in seconds) obtained after the consistency analysis of the large-scale regulatory networks and experimental datasets used to illustrate the BioQuali plugin. We compared the results obtained with our plugin to those obtained with the COMA plugin using the same data. Using BioQuali, we obtained four types of results: local inconsistencies (LI), global inconsistencies (GI), only network consistency (Cons.), or predictions (Pred.). Using the COMA plugin only local inconsistencies are reported. The difference in the types of results is reflected in the time the plugins took to perform the computation. We tested the time performance with a standard PC.