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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)

From: Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat

  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)
  1. aHuman GWAS variants associated with Obesity and Metabolic traits in the NHGRI-EBI GWAS catalogue
  2. bGenes expressed specifically in liver according to UniProt tissue database and accessed by using DAVID web services
  3. cGenes differently expressed in liver or in kidney when comparing the susceptible Lyon rats (LH or LL) with the control Lyon rat (LH)
  4. Numbers of human orthologues having evidence of associations with insulin resistance, dyslipidaemias and obesity are shown between parentheses