Table 2.
Number of rat genes and human orthologues expressed in liver of the susceptible Lyon rats (LH or LL) and associated with coding or promoter strain-specific variation overlapping HVRs with at least one conserved peak for three liver-specific transcription factors (i.e. the HVR 3TF subset)
| LHvsLN | LLvsLN | |||
|---|---|---|---|---|
| Rat genes | Human orthologues | Rat genes | Human orthologues | |
| Coding Variation | ||||
| Genes with NSC-SSVs | 133 | 111 (1, 1, 14) | 96 | 78 (0, 0, 8) |
| Genes with GWASa and NSC-SSVs | 3 | 2 (0, 0, 2) | 3 | 3 (0, 0, 2) |
| Liver-genesb with NSC-SSVs | 15 | 9 (0, 1, 4) | 10 | 6 (0, 0, 1) |
| Dif-liverc genes with NSC-SSVs | 14 | 12 (0, 0, 0) | 17 | 16 (0, 0, 1) |
| Dif-kidneyc genes with NSC-SSvs | 32 | 25 (0, 0, 4) | 9 | 7 (0, 0, 0) |
| Promoters | ||||
| Genes assigned to promoters with SSVs | 232 | 206 (7, 3, 32) | 189 | 164 (4, 4, 18) |
| Genes assigned to promoters with GWASa and SSVs | 1 | 1 (0, 0, 1) | 1 | 1 (0, 0, 1) |
| Liver-genesb assigned to promoters with SSVs | 35 | 30 (2, 1, 9) | 26 | 26 (1, 1, 4) |
| Dif-liverc assigned to promoters with SSVs | 38 | 33 (1, 1, 8) | 26 | 26 (1, 1, 3) |
| Dif-kidneyc assigned to promoters with SSVs | 52 | 44 (0, 1, 7) | 13 | 13 (0, 1, 1) |
aHuman GWAS variants associated with Obesity and Metabolic traits in the NHGRI-EBI GWAS catalogue
bGenes expressed specifically in liver according to UniProt tissue database and accessed by using DAVID web services
cGenes differently expressed in liver or in kidney when comparing the susceptible Lyon rats (LH or LL) with the control Lyon rat (LH)
Numbers of human orthologues having evidence of associations with insulin resistance, dyslipidaemias and obesity are shown between parentheses