Table 5.
Human Gene Expression Pathways Overexpressed in MS.
| Pathway | Ratio | # Genes in Pathway | # Differentially Expressed Genes: Identity | FDR (q) |
|---|---|---|---|---|
| Toll-Like Receptors Cascades | 0.0208 | 132 | 11: IL6R, CD14, LGMN, TLR2, TLR4, TLR7, ITGB2, ITGAM, IRAK3, CTSS, CTSL | <3.33e-04 |
| Trafficking and processing of endosomal TLR | 0.0019 | 12 | 4: LGMN, TLR7, CTSS, CTSL | 2.25e-03 |
| Innate Immune System | 0.1046 | 663 | 24: C1QC, C1QA, C1QB, FCER1G, IGLC7, WASF2, LYN, IL6R, WIPF1, IGLC2, CD14, LGMN, TLR2, TLR4, TLR7, HLA-E, ITGB2, ITGAM, IRAK3, CTSS, CTSL, TREM2, CD4, TXNIP | 3.20e-03 |
| Interferon gamma signaling | 0.0114 | 72 | 7: CD44, HLA-DRB1, CIITA, HLA-A, HLA-E, IFNGR1, PTAFR | 6.00e-03 |
| Endosomal/Vacuolar pathway | 0.0014 | 9 | 3: HLA-A, HLA-E, CTSS | 2.14e-02 |
| Integrin cell surface interactions | 0.0103 | 65 | 6: CD44, F11R, ITGB2, ITGB1, ITGAM, ITGAX | 2.75e-02 |
| Phosphorylation of CD3 and TCR zeta chains | 0.0043 | 27 | 4: HLA-DRB1, PAG1, CD4, PTPRC | 4.04e-02 |
| Platelet Adhesion to exposed collagen | 0.0021 | 13 | 3: FCER1G, LYN, ITGB1 | 4.95e-02 |
Bowtie (v2.2.5.0), tophat (v2.0.14) and cuffdiff (v2.2.1) were used to calculate differential expression levels of known splice variants in the demyelination and control sample groups12,13. Pathway enrichment of the differentially expressed genes was calculated with Cytoscape and the Reactome Curated Pathway Database16.