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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