Table 1 NEASE enrichment obtained from AS comparison between normal-appearing white matter and acute lesions, from multiple sclerosis patients. The highly enriched pathways belong to Neurotransmitter receptors, MAPK, and bacterial infection. Most of these pathways are hallmarks of MS. The NEASE score is obtained after combining the p value with the number of significant genes. The latter is obtained after individual tests for each gene in the column “Spliced genes” (see the “Methods” section)
Pathway name | Spliced genes (number of interactions affecting the pathway) | p value | adj p value | NEASE score |
|---|---|---|---|---|
Neurotransmitter receptors and postsynaptic signal transmission | GRIA1 (7), ATP2B1 (2), BRAF (4), MAP2K4 (1), GRIN1 (4) | 4.38e−09 | 0.000004 | 16.71 |
Uptake and function of anthrax toxins | ATP2B1 (1), BRAF (5), MAP2K4 (3) | 2.98e−09 | 0.000004 | 14.76 |
Transmission across chemical synapses | GRIA1 (7), ATP2B1 (2), BRAF (4), MAP2K4 (1), GRIN1 (4) | 5.65e−08 | 0.000010 | 14.49 |
Uptake and actions of bacterial toxins | ATP2B1 (1), BRAF (5), MAP2K4 (3) | 3.46e−08 | 0.000009 | 12.92 |
Neuronal system | GRIA1 (7), ATP2B1 (2), BRAF (4), MAP2K4 (1), GRIN1 (4) | 8.71e−07 | 0.000122 | 12.11 |
MAPK family signaling cascades | MYH10 (2), ATP2B1 (1), BRAF (17), MAP2K4 (5), GRIN1 (3) | 1.52e−06 | 0.000184 | 10.07 |
Activation of NMDA receptor and postsynaptic events | GRIA1 (2), ATP2B1 (1), BRAF (4), MAP2K4 (1), GRIN1 (3) | 2.12e−06 | 0.000241 | 9.82 |
FCERI mediated MAPK activation | MYH10 (1), BRAF (7), MAP2K4 (8) | 2.52e−07 | 0.000038 | 9.33 |
RAF/MAP kinase cascade | MYH10 (1), ATP2B1 (1), BRAF (16), MAP2K4 (4), GRIN1 (3) | 1.00e−06 | 0.000130 | 8.48 |
Signaling by moderate kinase activity BRAF mutants | MYH10 (1), BRAF (14), MAP2K4 (2) | 8.30e−09 | 0.000004 | 8.08 |