Table 2.
Pathways enriched in temporal patterns by SST
| Pathways from temporal up-pattern (KEGG ID) | P-value* | FDR** | Pathways from temporal down-pattern (KEGG ID) | P-value | FDR | ||
|---|---|---|---|---|---|---|---|
| All genes |
Simple enrichment analysis |
Cell cycle (mmu04110) |
8.41E-05 |
9.62E-03 |
Drug metabolism-cytochrome P450 (mmu00982) |
3.57E-10 |
3.07E-08 |
| Systemic lupus erythematosus (mmu05322) |
7.97E-10 |
3.43E-08 |
|||||
| Complement and coagulation cascades (mmu04610) |
3.45E-08 |
9.88E-07 |
|||||
| Retinol metabolism (mmu00830) |
4.38E-08 |
9.41E-07 |
|||||
| Metabolism of xenobiotics by cytochrome P450 (mmu00980) |
1.15E-06 |
1.97E-05 |
|||||
| Linoleic acid metabolism (mmu00591) |
2.04E-06 |
2.92E-05 |
|||||
| Prion diseases (mmu05020) |
2.43E-05 |
2.99E-04 |
|||||
| PPAR signaling pathway (mmu03320) |
3.42E-05 |
3.67E-04 |
|||||
| Drug metabolism-other enzymes (mmu00983) |
4.87E-04 |
4.64E-03 |
|||||
| Topology-based signaling pathway analysis |
|
|
|
Systemic lupus erythematosus (mmu05322) |
1.74E-10 |
1.36E-08 |
|
| Complement and coagulation cascades (mmu04610) |
4.55E-10 |
1.77E-08 |
|||||
| Cytokine-cytokine receptor interaction (mmu04060) |
1.69E-08 |
1.84E-06 |
Prion diseases (mmu05020) |
2.82E-07 |
7.33E-06 |
||
| Osteoclast differentiation (mmu04380) |
4.88E-06 |
2.66E-04 |
PPAR signaling pathway (mmu03320) |
1.42E-06 |
2.78E-05 |
||
| Cell cycle (mmu04110) |
1.52E-04 |
5.55E-03 |
Staphylococcus aureus infection (mmu05150) |
3.48E-06 |
5.42E-05 |
||
| |
|
|
Serotonergic synapse (mmu04726) |
1.18E-05 |
1.53E-04 |
||
| Alcoholism (mmu05034) |
2.48E-04 |
2.77E-03 |
|||||
| Endocrine and other factor-regulated calcium reabsorption (mmu04961) |
7.76E-04 |
7.57E-03 |
|||||
| MicroRNA targets |
Simple enrichment analysis |
No pathway |
|
|
Metabolism of xenobiotics by cytochrome P450 (mmu00980) |
1.45E-04 |
3.19E-03 |
| Topology-based signaling pathway analysis |
Cell cycle (mmu04110) |
5.46E-03 |
1.00E-02 |
No pathway |
|
|
|
| Non-microRNA targets |
Simple enrichment analysis |
No pathway |
|
|
Systemic lupus erythematosus (mmu05322) |
1.63E-10 |
1.22E-08 |
| Complement and coagulation cascades (mmu04610) |
9.24E-09 |
3.46E-07 |
|||||
| Drug metabolism (mmu00982) |
1.94E-07 |
4.85E-06 |
|||||
| Prion diseases (mmu05020) |
1.20E-05 |
2.26E-04 |
|||||
| Retinol metabolism (mmu00830) |
2.82E-05 |
4.22E-04 |
|||||
| Linoleic acid metabolism (mmu00591) |
2.01E-04 |
2.51E-03 |
|||||
| PPAR signaling pathway (mmu03320) |
8.76E-04 |
9.34E-03 |
|||||
| Topology-based signaling pathway analysis |
Cytokine-cytokine receptor interaction (mmu04060) |
1.63E-07 |
1.42E-05 |
Systemic lupus erythematosus (mmu05322) |
3.95E-11 |
3.00E-09 |
|
| Complement and coagulation cascades (mmu04610) |
1.31E-10 |
4.97E-09 |
|||||
| Prion diseases (mmu05020) |
1.32E-07 |
3.34E-06 |
|||||
| NF-kappa B signaling pathway (mmu04064) |
2.37E-05 |
8.95E-04 |
Staphylococcus aureus infection (mmu05150) |
1.63E-06 |
3.10E-05 |
||
| MAPK signaling pathway (mmu04010) |
3.09E-05 |
8.95E-04 |
Serotonergic synapse (mmu04726) |
5.15E-05 |
7.83E-04 |
||
| Osteoclast differentiation (mmu04380) |
4.17E-04 |
9.07E-03 |
PPAR signaling pathway (mmu03320) |
9.33E-05 |
1.18E-03 |
||
| Endocrine and other factor-regulated calcium reabsorption (mmu04961) |
6.65E-04 |
7.22E-03 |
|||||
| Alcoholism (mmu05034) | 9.07E-04 | 8.61E-03 |
*For simple enrichment analysis, the p values are calculated by the Fisher’s exact test in the DAVID program [30]. For topology-based signaling pathway analysis, the p value indicates the global pathway significance p value (PG), which combines the enrichment p values and the perturbation p values in regard to pathway topology with a random bootstrap iteration number of 3000 [31].
**The false discovery rate (FDR) correction is measured by applying the Benjamini algorithm [30,31].