Table 6.
Functional pathways of genes most affected by LPS stimulation, determined by using the Genomatix Pathway System (GePS)
|
LPS vs Ref 3 h (List of 147 genes taken into account) |
|
|
|---|---|---|
| p value | nb of genes* | |
|
Signal transduction pathways (canonical) |
|
|
| Fas signaling pathway |
7.58 × 10-6 |
5/20 |
|
Signal transduction pathways (Genomatix) |
p value |
nb of genes |
| NF kappa B |
1.52 × 10-12 |
41/1542 |
| Signal transducer and activator of transcription |
1.76 × 10-12 |
36/1184 |
| Toll like receptor |
2.49 × 10-12 |
26/593 |
| Apoptosis |
7.27 × 10-12 |
52/2592 |
| Tumor protein p53 |
8.23 × 10-12 |
34/1108 |
| Interleukin 1 |
2.05 × 10-11 |
27/706 |
| Janus kinase |
2.57 × 10-11 |
26/657 |
| Tumor necrosis factor |
5.10 × 10-11 |
34/1182 |
| Interleukin 6 |
5.57 × 10-11 |
26/680 |
| Inflammatory |
8.31 × 10-11 |
33/1133 |
| Nuclotide oligodimerization domain/ |
9.52 × 10-11 |
13/131 |
| Caspase recruitment protein family |
|
|
|
Molecular functions (GO) |
|
|
| Cytokine receptor binding |
2.29 × 10-9 |
12/187 |
| Receptor binding |
9.83 × 10-9 |
23/917 |
| Cytokine activity |
5.22 × 10-8 |
11/199 |
| Chemokine activity |
4.88 × 10-7 |
6/47 |
| Chemokine receptor binding |
9.02 × 10-7 |
6/52 |
|
Biological processes (GO) |
|
|
| Immune system process |
2.27 × 10-11 |
28/1094 |
| Immune response |
2.98 × 10-10 |
22/736 |
| Locomotion |
2.72 × 10-9 |
19/605 |
| Multi-organism process |
8.37 × 10-9 |
21/800 |
| Response to chemical stimulus |
1.67 × 10-8 |
28/1461 |
|
LPS vs Ref 6 h (List of 193 genes taken into account) |
|
|
|
Signal transduction pathways (Genomatix) |
|
|
| Signal transducer and activation |
8.41 × 10-17 |
44/1184 |
| NF-kB |
2.66 × 10-16 |
49/1542 |
| Chemokine (CC motif) ligand 2 |
8.63 × 10-16 |
23/272 |
| Interleukin 6 |
1.91 × 10-15 |
33/680 |
| Toll like receptor |
2.39 × 10-15 |
31/593 |
| Immune |
4.25 × 10-15 |
38/957 |
| Inflammatory |
4.85 × 10-15 |
41/1133 |
| Tumor necrosis factor |
2.14 × 10-14 |
41/1182 |
| Interleukin 1 |
2.87 × 10-13 |
31/706 |
| Janus kinase |
2.89 × 10-13 |
30/657 |
|
Molecular functions (GO) |
|
|
| Cytokine activity |
1.21 × 10-10 |
14/199 |
| Receptor binding |
3.74 × 10-9 |
25/917 |
| Cytokine receptor binding |
7.90 × 10-9 |
12/187 |
| Protein binding |
5.75 × 10-6 |
80/8067 |
|
Biological processes (GO) |
|
|
| Immune response |
1.59 × 10-14 |
29/736 |
| Immune system process |
3.15 × 10-13 |
33/1094 |
| Response to stress |
1.53 × 10-12 |
42/1880 |
| Defense response |
2.45 × 10-12 |
26/708 |
| Response to stimulus | 2.98 × 10-11 | 58/3713 |
* Nb of genes: number of genes in the list/number of genes in the pathway.