Table 2.
Strong cis-eQTLs mapping outside of known EAE QTLs in DA/PVG.1av1 crosses
| Chr | LODa | Meanb | Rat eQTLc | Genomicd | Gene symbol | Gene name |
|---|---|---|---|---|---|---|
| cis-eQTL | Expression | Probe set | Location | |||
| 1 | 27.2 | 117.7 | 10703445 | 56730912 | Fpr3 | Formyl peptide receptor 3 |
| 1 | 12.0 | 137.6 | 10703706 | 63694428 | Lilrb3 | Leukocyte immunoglobulin-like receptor, subfamily |
| 1 | 13.2 | 217.4 | 10719648 | 79504886 | Zfp61 | Zinc finger protein 61 |
| 1 | 10.3 | 519.0 | 10706297 | 93734935 | Siglec5 | Sialic acid-binding Ig-like lectin 5 |
| 1 | 12.9 | 348.9 | 10724073 | 159055461 | Art2 | t-Cell ecto-ADP-ribosyltransferase 1 |
| 1 | 16.6 | 78.5 | 10724164 | 159590904 | Chrna10 | Cholinergic receptor, nicotinic, alpha polypeptide |
| 1 | 13.3 | 59.8 | 10711944 | 198987150 | Lrrc27 | Leucine rich repeat containing 27 |
| 1 | 13.7 | 251.6 | 10728904 | 213828858 | Ms4a7 | Membrane-spanning 4-domains, subfamily A, member 7 |
| 1 | 10.1 | 355.8 | 10728918 | 214162552 | Ms4a6a | Membrane-spanning 4-domains, subfamily A, member 6 |
| 1 | 18.5 | 97.9 | 10714106 | 215590616 | Fam111a | Family with sequence similarity 111, member A (NP_001102633.1) |
| 2 | 14.6 | 413.1 | 10823903 | 173683154 | Gucy1b3 | Guanylate cyclase 1, soluble, beta 3 |
| 2 | 28.6 | 145.2 | 10816144 | 175479320 | Sfrp2 | Secreted frizzled-related protein 2 |
| 2 | 12.0 | 263.3 | 10824357 | 180974111 | Msto1 | Misato homolog 1 |
| 2 | 12.7 | 114.7 | 10824611 | 182644098 | Slc27a3 | Long-chain fatty acid transport protein 3 |
| 2 | 10.7 | 221.3 | 10819690 | 244323411 | Mcoln2 | Mucolipin 2 |
| 3 | 10.2 | 78.6 | 10844331 | 11511403 | Lcn2 | Lipocalin 2 |
| 3 | 12.3 | 168.9 | 10847957 | 90174952 | Prrg4 | Transmembrane gamma-carboxyglutamic acid protein 4 |
| 3 | 24.9 | 121.2 | 10848652 | 106548815 | Sptbn5 | Spectrin, beta, non-erythrocytic 5 |
| 4 | 11.4 | 400.7 | 10866507 | 173884317 | Art4 | Ecto-ADP-ribosyltransferase 4 |
| 4 | 10.0 | 334.6 | 10859337 | 174009860 | Pde6h | Phosphodiesterase 6H, cGMP-specific, cone, gamma |
| 5 | 14.9 | 136.4 | 10875425 | 24893573 | RGD1309085 | Similar to F23N19.9 |
| 5 | 10.2 | 114.7 | 10867761 | 32352311 | Mmp16 | Matrix metalloproteinase-16 |
| 5 | 10.9 | 62.8 | 10877130 | 77010784 | Ptgr1 | Prostaglandin reductase 1 |
| 5 | 10.8 | 586.7 | 10869288 | 77924255 | Snx30 | Sorting nexin family member 30 |
| 6 | 10.7 | 1359.5 | 10892653 | 142735827 | Igh-6 | Immunoglobulin heavy chain 6 |
| 6 | 25.7 | 267.3 | 10892662 | 142977680 | IgG-2a | Gamma-2a immunoglobulin heavy chain |
| 7 | 11.6 | 260.5 | 10904539 | 112913724 | Ly6k | Lymphocyte antigen 6 complex, locus K |
| 7 | 16.1 | 536.7 | 10904597 | 113434499 | Ly6a | Lymphocyte antigen 6 complex, locus A (predicted) |
| 7 | 15.0 | 509.1 | 10898196 | 121816012 | Mpped1 | Metallophosphoesterase domain containing 1 |
| 9 | 16.3 | 127.8 | 10929288 | 79091425 | Serpine2 | Serine (or cysteine) proteinase inhibitor, clade E |
| 11 | 10.5 | 34.5 | 10751434 | 66357714 | Csta | Cystatin A (stefin A) |
| 11 | 12.6 | 76.6 | 10754876 | 70653993 | LOC684506 | Similar to SMP3 mannosyltransferase |
| 12 | 15.8 | 109.3 | 10762254 | 36896819 | Oas1k | 2′–5′ oligoadenylate synthetase 1K |
| 13 | 29.0 | 158.8 | 10769672 | 85533882 | Rgs4 | Regulator of G-protein signaling 4 |
| 13 | 10.2 | 301.6 | 10765469 | 86096465 | Sh2d1b1 | Similar to EWS/FLI1 activated transcript 2 |
| 14 | 24.2 | 135.0 | 10776325 | 33403956 | LOC498350 | Similar to testicular haploid expressed gene product isoform 2 |
| 14 | 10.3 | 45.5 | 10778820 | 109197351 | Ccdc85a | Coiled-coil domain containing 85A |
| 16 | 17.5 | 229.3 | 10787757 | 22852487 | Csgalnact1 | Chondroitin sulfate N-acetylgalactosaminyltransferase 1 |
| 16 | 26.5 | 409.1 | 10789670 | 84885522 | Lig4 | DNA ligase 4 |
| 18 | 15.4 | 140.2 | 10804396 | 40914028 | Cdo1 | Cysteine dioxygenase 1, cytosolic |
| X | 14.4 | 236.7 | 10936742 | 21117225 | GPR34 | G-protein-coupled receptor GPR34 (predicted) |
| X | 16.9 | 73.6 | 10937013 | 26697034 | Kcnd1 | Potassium voltage-gated channel, Shal-related subfamily, member 1 |
| X | 26.8 | 106.0 | 10932773 | 35143324 | Chrdl1 | Kohjirin |
| X | 11.8 | 68.2 | 10939319 | 122209367 | Armcx6 | Armadillo repeat containing, X-linked 6 |
| X | 12.8 | 209.6 | 10939498 | 127688736 | LOC678934 | Similar to CG30327-PA |
eQTLs were selected to have a logarithm of odds (LOD) score ≥ 10 and a genome-wide corrected P-value ≤0.05 (generated with 1000 permutations). Cis-eQTLs were considered those having no genetic marker between the peak of the linkage score and the chromosomal region coding the transcript. Genes in bold are differentially expressed between DA and PVG in day 7 post-immunization ex vivo LN cells and/or in MOG re-stimulated conditions (49).
Abbreviations: QTL, quantitative trait locus; LOD, logarithm of the odds ratio; eQTL, expression quantitative trait locus; Chr, chromosome.
aLOD score of cis-eQTL for probe sets generated with the Haley–Knott regression model, no covariates, in R/qtl.
bAverage probe set expression level.
cProbe ID annotation from Affymetrix Rat Gene 1.0 ST array.
dGenomic location of the transcript, start, in mega base pairs.