Table 3.
Significant pathways from PHARAOH in the replication study
| DB | Pathway | PHARAOH |
|---|---|---|
| Biocarta | HIV-I Nef: negative effector of Fas and TNF | 0.006 |
| Feeder pathways for glycolysis | 0.016 | |
| Human cytomegalovirus and map kinase pathways | 0.018 | |
| Lck/Fyn tyrosine kinases in initiation of TCR Activation | 0.022 | |
| Erythrocyte differentiation pathway | 0.026 | |
| NFkB activation by Nontypeable Hemophilus influenza | 0.048 | |
| Growth hormone signaling pathway | 0.049 | |
| Influence of Ras and Rho proteins on G1 to S Transition | 0.049 | |
| KEGG | Glycine, serine and threonine metabolism | 0.01 |
| Metabolism of xenobiotics by cytochrome P450 | 0.018 | |
| Insulin signaling pathway | 0.028 | |
| Glycosaminoglycan biosynthesis (keratan sulfate) | 0.032 | |
| Phenylalanine metabolism | 0.036 | |
| Tryptophan metabolism | 0.044 |
Pathway names with bold text and underlined text indicate the replicated pathways in the independent dataset using the same pathway database, an independent dataset and a different pathway database (SP), respectively.