Table 2.
Positional candidate genes differentially expressed between LG/J and SM/J soleus muscles
| Chr | QTL | Probe set ID | Gene | P Value | Fold-Change | Gene Name |
|---|---|---|---|---|---|---|
| 2 | Mfq4 | 17393868 | Mafb | 0.033 | −1.77 | v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (avian) |
| 17393910 | Chd6 | 0.042724 | −1.13 | chromodomain helicase DNA binding protein 6 | ||
| 17404652 | Gm24780 | 0.032914 | −1.98 | predicted gene Gm24780, predicted protein is B4HDV3 | ||
| 3 | Mfq5 | 17396801 | Ttc14 | 0.033387 | −1.14 | tetratricopeptide repeat domain 14 |
| 17396876 | 0.0219376 | −1.80 | there are no assigned mRNA sequences for this probe set; the probe set lies within lncRNA Sox2ot (Sox2 overlapping transcript, nonprotein coding) | |||
| 17425606 | Gm12526 | 0.046791 | −1.17 | predicted gene 12526 | ||
| 17414380 | Gm24277 | 0.00525644 | −2.07 | Gm24277, a known snRNA; the probe set also lies within an intronic region of RefSeq gene Pakap (PALM2-AKAP2), a read-through transcript on chromosome 4 | ||
| 17425701 | Mir3095 | 0.0298235 | −1.78 | Mir3095 (Entrez ID 100526502; EST ENSMUST00000175552). | ||
| 17426097 | Mup3 | 0.00304 | −1.49 | major urinary protein 3 | ||
| 17426126 | Fkbp15 | 0.018038 | −1.10 | FK506 binding protein 15 | ||
| 4 | Mfq6 | 17414545 | Slc31a1 | 0.049799 | 1.12 | solute carrier family 31, member 1 |
| 17426166 | Cdc26 | 0.021407 | −1.29 | cell division cycle 26 | ||
| 17426198 | Hdhd3 | 0.000869 | 1.86 | haloacid dehalogenase-like hydrolase domain containing 3 | ||
| 17426206 | Alad | 9.75E-05 | 1.91 | aminolevulinate, delta-, dehydratase | ||
| 17414600 | Rgs3 | 0.023096 | 1.08 | regulator of G protein signaling 3 | ||
| 17248064 | Mtif2 | 0.015517 | −1.16 | mitochondrial translational initiation factor 2 | ||
| 17261285 | LOC102637613 | 0.00432682 | 1.68 | linc RNA [AK084560 (EST)/ Gm12092 (predicted gene)]. | ||
| 17248127 | 0.00187422 | −1.46 | there are no assigned mRNA sequences for this transcript; the probe set lies within an intron of Sptbn1 | |||
| 11 | Mfq3 | 17261393 | Acyp2 | 0.011777 | 1.26 | acylphosphatase 2, muscle type |
| 17248196 | Asb3 | 0.014221 | −1.15 | ankyrin repeat and SOCS box-containing 3 |
P Value, ANOVA P value for strain effect; fold change uses SM/J as baseline (negative values indicate LG/J expression is down compared with SM/J, positive values LG/J expression up compared with SM/J); boldface indicates that gene is predominantly and/ or strongly expressed in skeletal muscle tissue (79). “Gene Name,” for probe sets not designed against an annotated gene, genes at the genomic loci of the Affymetrix probe set were identified in UCSC genome browser using mouse genome build GRCm38.