Table 6. Details of the hits of canonical pathway CD28 Signaling in T Helper Cells.
Official symbols of the significant genes found via RNA-Seq (RIP-Seq) that are in the pathway (Fig 3) is given along with the name of its corresponding node in the pathway. Fold is given as KO/CTL (RNA-Seq) or IP/CTL (RIP-Seq), and q is the false discovery rate value based on method of Benjamini-Hochberg. Genes were identified by both RNA-Seq and RIP-Seq. Numbers in parentheses and italicized denote data obtained from RIP-Seq.
| Symbol | Member of Node | Entrez Gene Name | RNA (RIP) Fold | RNA (RIP) q |
|---|---|---|---|---|
| AKT1 | AKT | v-akt murine thymoma viral oncogene homolog 1 | 0.887 | 0.140 |
| ARPC4 | ARP2/3 | actin related protein 2/3 complex, subunit 4, 20kDa | 1.108 | 0.088 |
| ATM | ATM | ataxia telangiectasia mutated | 0.905 | 0.189 |
| Calm1 | CALM | calmodulin 1 | 1.132 | 0.153 |
| CAMK4† | CALM | calcium/calmodulin-dependent protein kinase IV | 0.85 (637) | 0.06 (<1E-99) |
| CD80 | CD80/CD86 | CD80 molecule | 0.861 | 0.159 |
| CD3D | CD3 | CD3d molecule, delta (CD3-TCR complex) | 1.184 | 0.108 |
| CD3G | CD3 | CD3g molecule, gamma (CD3-TCR complex) | 1.178 | 0.026 |
| HLA-DMA* | MHC II | major histocompatibility complex, class II, DM alpha | (2196) | (<1E-99) |
| HLA-DMB | MHC II | major histocompatibility complex, class II, DM beta | 1.215 | 0.249 |
| HLA-DOA | MHC II | major histocompatibility complex, class II, DO alpha | 1.194 | 0.263 |
| HLA-DOB | MHC II | major histocompatibility complex, class II, DO beta | 0.622 | <1E-3 |
| IKBKE | IKK | inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon | 0.868 | 0.244 |
| IKBKG | IKK | inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma | 0.935 | 0.282 |
| IL2 | IL-2 | interleukin 2 | 1.933 | 0.103 |
| ITK | ITK | IL2-inducible T-cell kinase | 0.912 | 0.244 |
| ITPR1 | IP3R | inositol 1,4,5-trisphosphate receptor, type 1 | 0.806 | 0.221 |
| ITPR3 | IP3R | inositol 1,4,5-trisphosphate receptor, type 3 | 0.881 | 0.258 |
| MAPK9 | JNK | mitogen-activated protein kinase 9 | 0.864 | 0.010 |
| NFKB2 | NFκB | nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) | 1.096 | 0.285 |
| NFKBIE | IκB | nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon | 1.089 | 0.111 |
| PIK3C2A | PI3K | phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha | 0.627 | 0.017 |
| PLCG1 | PLCγ1 | phospholipase C, gamma 1 | 0.891 | 0.220 |
| PPP3CA | Calcineurin | protein phosphatase 3, catalytic subunit, alpha isozyme | 1.264 | 0.049 |