Table 2 Overrepresented pathways in prioritised SNP selection a .

From: A systematic SNP selection approach to identify mechanisms underlying disease aetiology: linking height to post-menopausal breast and colorectal cancer risk

Pathways

Set size

Number of genes from set in annotated gene list

Genes

p-value

q-value b

Pathway source

Overrepresented pathways using the genes annotated to the prioritised set of SNPs associated with height, post-menopausal breast and colorectal cancer risk.

 Hedgehog signalling pathway

52

4

BMP2, STK36, IHH, PTCH1

7.78 × 10−7

2.08 × 10−5

KEGG

 Hedgehog signalling pathway

16

3

STK36, IHH, PTCH1

1.49 × 10−6

2.08 × 10−5

Wikipathways

 Hedgehog

25

3

STK36, IHH, PTCH1

6.06 × 10−6

5.56 × 10−5

NetPath

 Ligand-receptor interactions

8

2

IHH, PTCH1

5.76 × 10−5

3.77 × 10−4

Reactome

 Basal cell carcinoma

55

3

BMP2, STK36, PTCH1

6.73 × 10−5

1.63 × 10−3

KEGG

 HH-Core

19

2

IHH, PTCH1

3.48 × 10−4

1.63 × 10−3

Signalink

 Signalling events mediated by the Hedgehog family

23

2

IHH, PTCH1

5.14 × 10−4

2.06 × 10−3

PID

 Hedgehog, on, state

42

2

IHH, PTCH1

1.41 × 10−3

4.93 × 10−3

Reactome

 Hedgehog signalling events mediated by Gli proteins

50

2

STK36, PTCH1

2.24 × 10−3

6.97 × 10−3

PID

 Endochondral ossification

64

2

IHH, PTCH1

3.83 × 10−3

1.07 × 10−3

Wikipathways

 TGF-beta signalling pathway

80

2

BMP2, ID4

5.96 × 10−3

1.48 × 10−3

KEGG

 Signalling by Hedgehog

87

2

IHH, PTCH1

6.41 × 10−3

1.48 × 10−3

Reactome

 Class B/2 (Secretin family receptors)

88

2

IHH, PTCH1

6.87 × 10−3

1.48 × 10−3

Reactome

Overrepresented pathways using the genes annotated to the prioritised SNPs associated with height and post-menopausal breast cancer risk.

 Hedgehog signalling pathway

16

2

STK36, IHH

1.13 × 10−4

1.35 × 10−3

Wikipathways

 Hedgehog

25

2

STK36, IHH

2.81 × 10−4

1.68 × 10−3

NetPath

 Hedgehog signalling pathway

52

2

STK36, IHH

1.18 × 10−3

4.70 × 10−3

KEGG

 Signalling by ERBB4

153

2

ESR1, TNRC6B

9.02 × 10−3

2.19 × 10−2

Reactome

 Androgen receptor

149

2

ESR1, ZMIZ1

9.14 × 10−3

2.19 × 10−2

NetPath

Overrepresented pathways using the genes annotated to the prioritised SNPs associated with height and colorectal cancer risk.

 Hedgehog signalling pathway

52

2

BMP2, PTCH1

2.81 × 10−4

6.34 × 10−4

KEGG

 Basal cell carcinoma

55

2

BMP2, PTCH1

2.53 × 10−4

6.34 × 10−4

KEGG

  1. Abbreviations: SNP, single nucleotide polymorphism.
  2. aOverrepresented pathways were retrieved using the SNP-gene annotations from GRAIL.
  3. bThe p-values are corrected for multiple testing using the false discovery rate method and are shown as q-values.
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