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Table 3 A statistical comparison of central carbon metabolism modules

From: AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response

 

ambient

GiGA

Glycolysis/Gluconeogenesis - top

  

Module

u2

u2

Recall

.67

.89

Precision

.33

.23

F-measure

.44

.36

TCA Cycle

  

Module

u1

u1

Recall

.94

.63

Precision

.19

.13

F-measure

.32

.22

GLY/GLN - TCA connection pathway

  

Module

d1

d1

Recall

.86

.29

Precision

.03

.05

F-measure

.05

.09

  1. Values of recall, precision and F-measure for the comparison between the two computational inference methods for metabolic modules and the expert curation of DeRisi et al. [13]. The modules containing the relevant parts of metabolism for each computational method are indicated on the table, where ‘u’ and ‘d’ represent up- and down-regulated modules and the number corresponds to the numbers of the modules found in order of significance by the two methods. Diagrams for these can be found in the Additional file 2 except ambient u1, which can be seen in Figure 2.