Table 5 Results and annotations for the 5 autosomal genes associated with SAT mass and 1 autosomal gene associated with SAT/TAT in the Mendelian Randomization analysis that were replicated in the UK Biobank analysis.

From: Identification of novel genes whose expression in adipose tissue affects body fat mass and distribution: an RNA-Seq and Mendelian Randomization study

Gene information

Gene expression analysis

Mendelian Randomization analysis

Replication analysis

Trait

Ensembl

Gene

Chr

Start

End

Novel

Protein

beta

SE

p value

no_var

R2

p value

no_var

R2

p value

SAT

ENSG00000003249

DBNDD1

16

90004865

90020128

YES

Dysbindin domain-containing protein 1

0,30

0,06

2,79 × 10−7

333

0,87

5,31 × 10−4

11

0,151

3,13 × 10−3

SAT

ENSG00000060656

PTPRU

1

29236516

29326813

YES

Receptor-type tyrosine-protein phosphatase U

0,34

0,06

4,97 × 10−8

39

0,03

5,05 × 10−3

1

0,012

2,63 × 10−4

SAT

ENSG00000164307

ERAP1

5

96760810

96808100

NO

Endoplasmic reticulum aminopeptidase 1

0,36

0,07

8,37 × 10−7

368

0,88

6,26 × 10−11

15

0,349

3,70 × 10−2

SAT

ENSG00000166839

ANKDD1A

15

64911902

64958700

YES

Ankyrin repeat and death domain-containing protein 1 A

0,37

0,06

8,39 × 10−11

128

0,29

1,09 × 10−2

6

0,077

2,37 × 10−2

SAT

ENSG00000227082

LINC02798

1

121396754

121463129

YES

--

0,32

0,06

5,82 × 10−7

250

0,57

4,38 × 10−6

1

0,001

2,63 × 10−4

SAT/TAT

ENSG00000078070

MCCC1

3

183015218

183116075

YES

Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial

0,27

0,05

1,02 × 10−7

164

0,30

2,85 × 10−2

2

0,037

4,16 × 10−2

  1. Shown are the Ensembl ID of the gene (“Ensembl”), the gene symbol (“Gene”), the genomic position in form of the chromosome number (“Chr”) as well as the start (“Start”) and end (“End”) position in base pairs of the gene; whether the gene is known to be associated with obesity (based on the NCBI gene,GWAS Catalog and AstraZeneca PheWAS Portal databases), the corresponding protein encoded by the gene if it is known (from UniProt); and results of the statistical analyses: the estimates of the effect size (“beta”; estimate of beta_j in the marginal model of C-JAMP in Eq. (1), or (2) respectively, in the main text) its standard error estimates (“SE”) and p value (“p value”) from the C-JAMP association analysis of SAT and SAT/TAT conditional on the gene expression and covariates; the results from the Mendelian randomization (MR) analysis in form of the number of SNVs in the gene that were incorporated in the MR analysis (“no_var”), the explained variance of the gene expression based on a multiple linear regression model containing these SNVs (“R2”), and the p value from the inverse-variance weighted MR method (“p value”); as well as the results of the replication analysis in form of the number of SNVs in the gene that were incorporated in the MR analysis (“no_var”), the explained variance of the gene expression based on a multiple linear regression model containing these SNVs (“R2”), and the p value from the linear regression analysis (“p value”).
  2. The following gene ontology terms of the Biological Process (BP) ontology are associated with each of the genes, obtained using the annFUN.org() function in the topGO R package:
  3. DBNDD1: --
  4. PTPRU: protein dephosphorylation; cell adhesion; transmembrane receptor protein tyrosine phosphatase signaling pathway; negative regulation of cell proliferation; cell differentiation; negative regulation of cell migration; animal organ regeneration; homotypic cell-cell adhesion; protein localization to cell surface; peptidyl-tyrosine dephosphorylation; response to glucocorticoid; negative regulation of canonical Wnt signaling pathway; positive regulation of cell-cell adhesion mediated by cadherin
  5. ERAP1: angiogenesis; adaptive immune response; antigen processing and presentation of peptide antigen via MHC class I; membrane protein ectodomain proteolysis; regulation of blood pressure; response to bacterium; antigen processing and presentation of endogenous peptide antigen via MHC class I; regulation of innate immune response; fat cell differentiation; positive regulation of angiogenesis
  6. ANKDD1A: signal transduction
  7. LINC02798: --
  8. MCCC1: leucine catabolic process; biotin metabolic process; branched-chain amino acid catabolic process; protein heterooligomerization
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