Table 4. The top canonical pathways and the genes from our dataset after functional enrichment of the genes obtained from expression pairing in IPA.
| Canonical pathways | ↓Down | ↑Up | −log(p-value) | Genes | miR:RNA-seq Target Molecules (total # of significant mRNAs in pathway from RNA-seq) |
|---|---|---|---|---|---|
| α-tocopherol Degradation | 2/4 (50%) | 0/4 (0%) | 4.22E00 | 2 | CYP4F3, CYP4F2 |
| Allograft Rejection Signaling | 0/73 (0%) | 4/73 (5%) | 4.06E00 | 4 | HLA-DQA1, HLA-DRB3, PRF1, GZMB |
| Dendritic Cell Maturation | 0/176 0% | 5/176 (3%) | 3.61E00 | 5 | STAT4, HLA-DQA1, HLA-DRB3, PLCH2, CD1C |
| Graft-versus-Host Disease Signaling | 0/46 (0%) | 3/46 (7%) | 3.37E00 | 3 | HLA-DQA1, PRF1, GZMB |
| Autoimmune Thyroid Disease Signaling | 0/47 (0%) | 3/47 (6%) | 3.34E00 | 3 | HLA-DQA1, PRF1,GZMB |
| Granzyme B Signaling | 0/16 (0%) | 2/16 (13%) | 2.93E00 | 2 | PRF1, GZMB |
| T Helper Cell Differentiation | 0/69 (0%) | 3/69 (4%) | 2.86E00 | 3 | STAT4, HLA-DQA1, TBX21 |
| Basal Cell Carcinoma Signaling | 0/72 (0%) | 3/72 (4%) | 2.8E00 | 3 | WNT3, HKR1, WNT10B |
| Axonal Guidance Signaling | 0/432 (0% | 6/432 (1%) | 2.6E00 | 6 | WNT3, SEMA6B, PLCH2, HKR1, ADAMTS1, WNT10B |
| Role of MΦ, Fibroblasts and Endothelial Cells in RA | 1/297 (0%) | 4/297 (1%) | 2.59E00 | 5 | WNT3, F2RL1, CCL5, PLCH2, WNT10B |
| Tumoricidal Function of Hepatic Natural Killer Cells | 0/24 (0%) | 2/24 (8%) | 2.58E00 | 2 | PRF1, GZMB |
| Communication between Innate and Adaptive Immune Cells | 0/91 (0%) | 3/91 (3%) | 2.51E00 | 3 | CD8A, CCL5, HLA-DRB3 |
| Cytotoxic T Lymphocyte-mediated Apoptosis of Target Cells | 0/32 (0%) | 2/32 (6%) | 2.33E00 | 2 | PRF1, GZMB |
| Type I Diabetes Mellitus Signaling | 0/108 0% | 3/108 (3%) | 2.3E00 | 3 | HLA-DQA1, PRF1, GZMB |
| Antigen Presentation Pathway | 0/37 (0%) | 2/37 (5%) | 2.21E00 | 2 | HLA-DQA1, HLA-DRB3 |
| Complement System | 0/37 (0%) | 2/37 (5%) | 2.21E00 | 2 | C1QB, C1QA |
| Choline Degradation I | 0/2 (0%) | 1/2 (50%) | 2.2E00 | 1 | CHDH |
| Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses | 0/125 (0%) | 3/125 (2%) | 2.13E00 | 3 | CCL5, C1QB, C1QA |
| Human Embryonic Stem Cell Pluripotency | 0/133 (0% | 3/133 (2%) | 2.06E00 | 3 | WNT3, WNT10B, S1PR5 |
| Glioblastoma Multiforme Signaling | 0/146 0% | 3/146 (2%) | 1.95E00 | 3 | WNT3, PLCH2, WNT10B |
| Role of IL-17A in Arthritis | 0/54 (0%) | 2/54 (4%) | 1.89E00 | 2 | CCL5, CXCL3 (of 6) |
| Dopamine-DARPP32 Feedback in cAMP Signaling | 1/161 (1%) | 2/161 (1%) | 1.83E00 | 3 | KCNJ2, PPP1R14A, PLCH2 |
| Protein Citrullination | 1/5 (20%) | 0/5 (0%) | 1.8E00 | 1 | PADI2 |
| PCP pathway | 0/63 (0%) | 2/63 (3%) | 1.76E00 | 2 | WNT3, WNT10B |
| Granulocyte Adhesion and Diapedesis | 0/177 (0% | 3/177 (2%) | 1.72E00 | 3 | CCL5, CXCL3, CXCL2 |
| Agranulocyte Adhesion and Diapedesis | 0/189 (0% | 3/189 (2%) | 1.65E00 | 3 | CCL5, CXCL3, CXCL2 |
| OX40 Signaling Pathway | 0/76 (0%) | 2/76 (3%) | 1.61E00 | 2 | HLA-DQA1, HLA-DRB3 |
The rankings are based on the p values, starting with the lowest.