Table 4.
Top canonical pathways associated with Network A
| Ingenuity top canonical pathway | Ratioa | Genesb | P-valuec | Corrected P-valued |
|---|---|---|---|---|
| T Cell receptor signaling | 11/109 | CD247,CD3G,CD28,LCK,CAMK4,PRKCQ,CD3E,CD8A,CD3D,CD8B,ITK | 2.1E−15 | 3.1E−13 |
| iCOS–iCOSL signaling in T helper cells | 10/122 | CD247,CD3G,CD28,LCK,CD40LG,CAMK4,PRKCQ,CD3E,CD3D,ITK | 1.3E−13 | 9.6E−12 |
| CD28 signaling in T helper cells | 9/132 | CD247,CD3G,CD28,LCK,CAMK4,PRKCQ,CD3E,CD3D,ITK | 1.6E−11 | 7.9E−10 |
| Calcium-induced T lymphocyte apoptosis | 7/70 | CD247,CD3G,LCK,CAMK4,PRKCQ,CD3E,CD3D | 1.3E−10 | 4.8E−09 |
| Role of NFAT in regulation of the immune response | 9/200 | CD247,CD3G,CD28,LCK,CAMK4,PRKCQ,CD3E,CD3D,ITK | 4.8E−10 | 1.4E−08 |
Transcripts in Network A were uploaded into the ingenuity pathways application (Ingenuity Systems, www.ingenuity.com). The software was used to identify the most significant pathways.
aRatio refers to the number of molecules in a given pathway that meet cutoff criteria, divided by the total number of genes that map to the canonical pathway.
bGenes in a given pathway that meet cutoff criteria.
cSignificance was determined from a single test P-value calculated using the right-tailed Fisher's exact test.
dAdjusted significance was determined from multiple test-corrected P-values using the Benjamini–Hochberg correction (top five categories reaching a corrected statistical significance of ≤0.05 are shown).