Table 1

The results of TRS Network analysis.

Networks or pathways

Network score (p value)

S

P

|ε|

TLR4 TRS Network

4.312 (<1.0e-03)

17.246

942.988

218

TNF TRS Network

4.046 (<1.0e-03)

17.509

698.589

214

TLR signaling pathway

2.078 (0.38)

5.173

32.789

213

Apoptosis

1.385 (0.83)

3.958

159.534

158

D2D network

0.118 (0.99)

29.244

32.089

834

jActiveModule network

-0.194 (0.99)

41.025

19.484

970

The network scores are calculated by summing InS, and InP and subtracting In|| (See Eq. (5)). S indicates how much its nodes are differentially expressed. is calculated by summing the path scores of all TRS Pathways the network includes. P Sub-networks results are highlighted in bold to be easily recognized from KEGG pathway results. P values are assessed by random permutation of the expression of individual genes. The expression condition is 2h after the LPS treatment.

Hwang et al. BMC Bioinformatics 2011 12:19   doi:10.1186/1471-2105-12-19