Table 3:
Pathways commonly associated with all ANCA-associated vasculitis gene expression studies
| Pathway | Peripheral leukocytes |
Nasal sinus brushing |
Orbital tissue | md-locfdr * |
|---|---|---|---|---|
| Innate Immunity | ||||
| Neutrophil degranulation(R) | p=3.14×10−13 | p= 1.11×10−16 | p=3.28×10−09 | 1.05×10−12 |
| Antimicrobial peptides(R) | p=7.69×10−06 | p=1.13×10−03 | p=1.14×10−03 | 8.23×10−03 |
| Toll-Like Receptors Cascades(R) | p=1.85×10−05 | p=2.78×10−04 | p=3.39×10−03 | 0.026 |
| Phagosome(K) | p=0.477 | p=2.88×10−08 | p=0.021 | 3.165×10−03 |
| Interferon gamma signaling(R) | p=0.533 | p=0.733 | p=6.9×10−03 | 0.134 |
| Adaptive Immunity | ||||
| Signaling by the B Cell Receptor (BCR)(R) | p=0.774 | p=0.867 | p=6.68×10−03 | 0.022 |
| Vascular wall interactions | ||||
| Cell surface interactions at the vascular wall(R) | p=0.887 | p=4.49×10−04 | p=5.86×10−05 | 4.19×10−04 |
| amb2 Integrin signaling(N) | p=0.276 | p=1.90×10−06 | p=0.041 | 0.086 |
| Leukocyte transendothelial migration(K) | p=0.34 | p=2.94×10−04 | p=6.98×10−03 | 0.178 |
| Cellular signaling | ||||
| Signaling by Interleukins(R) | p=8.91×10−05 | p=8.24×10−08 | p=1.88×10−05 | 6.13×10−04 |
| Cytokine-cytokine receptor interaction(K) | p=6.66×10−03 | p=7.78×10−06 | p=4.08×10−04 | 0.036 |
| Chemokine signaling pathway(K) | p=0.308 | p=1.97×10−06 | p=0.013 | 0.041 |
| IL4-mediated signaling events(N) | p=5.47×10−04 | p=0.107 | p=5.04×10−04 | 0.021 |
| Complement Activation | ||||
| Complement and coagulation cascades(K) | p=0.199 | p=2.70×10−07 | p=0.048 | 0.044 |
| Tissue Damage/Tissue Repair | ||||
| Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling(N) | p=0.354 | p=9.81×10−08 | p=9.39×10−03 | 7.77×10−03 |
| Extracellular matrix organization(R) | p=0.497 | p=2.51×10−04 | p=1.27×10−03 | 0.024 |
| Platelet Activation | ||||
| Response to elevated platelet cytosolic Ca2+(R) | p=0.670 | p=4.50×10−06 | p=0.095 | 0.038 |
| GPVI-mediated activation cascade(R) | p=0.400 | p=2.1×10−03 | p=1.69×10−03 | 0.079 |
| Platelet homeostasis(R) | p=0.024 | p=0.656 | p=3.28×10−03 | 0.091 |
| Infectious Disease Pathways | ||||
| Leishmaniasis(K) | p=0.041 | p=1.22×10−09 | p=0.172 | 3.54×10−03 |
| Malaria(K) | p=0.340 | p=3.77×10−06 | p=1.69×10−03 | 0.012 |
| Tuberculosis(K) | p=0.040 | p=3.79×10−08 | p=2.52×10−03 | 0.019 |
| Measles(K) | p=0.759 | p=0.012 | p=2.84×10−03 | 0.035 |
| Amoebiasis(K) | p=5.97×10−04 | p=1.42×10−05 | p=0.080 | 0.142 |
| Other | ||||
| Osteoclast differentiation(K) | p=0.013 | p=6.19×10−12 | p=0.391 | 3.75×10−05 |
| Inflammatory bowel disease (IBD)(K) | p=4.91×10−03 | p=0.031 | p=5.8 ×10−04 | 0.093 |
| Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds(R) | p=1.12×10−03 | p=0.540 | p=0.01 | 0.124 |
| Syndecan-4-mediated signaling events(N) | p=0.283 | p=3.18×10−04 | p=4.47×10−03 | 0.155 |
*
md-localFDR = multi-dimensional local false discovery rate which can be thought of as the probability of individual pathway being a false discovery in all three tissues.
C = CellMap, R = Reactome, K = Kyoto Encyclopedia of Genes and Genomes (KEGG), N = National Cancer Institute Pathway Interaction Database (NCI PID)