Table 1

Properties of the PPI networks used for the evaluation of MCL-CAw

PPI Network

# Proteins

# Interactions

Avg node degree


Gavin

1430

7592

10.62

Krogan 'Core'

2708

7123

5.26


Gavin+Krogan

2964

13507

9.12

ICD(Gavin+Krogan)

1628

8707

10.69

FSW(Gavin+Krogan)

1628

8688

10.67

Consolidated3.19

1622

9704

11.96

Bootstrap0.094

2719

10290

7.56


Inferred

954

11892

24.93

Gavin+Krogan+Inferred

3418

25352

14.83

ICD(Gavin+Krogan+Inferred)

2034

12009

11.81

FSW(Gavin+Krogan+Inferred)

1892

11705

12.37


The Gavin+Krogan network was generated by combining the Gavin and Krogan-Core datasets, obtained from BioGrid [32]. The ICD(Gavin+Krogan) and FSW(Gavin+Krogan) networks were generated by scoring the Gavin+Krogan network using the Iterative-CDk and FS Weightk schemes [14,15] (with k = 2 iterations). The Consolidated3.19 network refers to the high-confidence subset (PE cut- off: 3.19) of the Consolidated network derived by Collins et al. [11]. The Bootstrap0.094 network refers to the high-confidence subset (BT cut-off: 0.094) of the Bootstrap network derived by Friedel et al. [17]. The Inferred network comprised of computationally inferred interactions from the Predictome database [40]. The Gavin+Krogan+Inferred network was generated by augmenting the Gavin+Krogan network with these inferred interactions. The ICD(Gavin+Krogan+Inferred) and FSW(Gavin+Krogan+Inferred) networks were generated by scoring this augmented network using the Iterative-CD and FS Weight systems, respectively.

Srihari et al. BMC Bioinformatics 2010 11:504   doi:10.1186/1471-2105-11-504

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