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Table 3 Top ranking pathways of genome-wide pathway analysis using regulatory SNPs

From: A genome-wide association scan on estrogen receptor-negative breast cancer

  

P-value distribution of SNPs

  

Pathway name (KEGG ID)

Class

SRT P

P < 0.01

0.01 ≤ P< 0.05

0.05 ≤ P< 0.1

N

Pof most significant SNP in pathway

Glioma (hsa05214)

Cancers

0.0394

1

5

4

26

0.0028

Long-term potentiation (hsa04720)

Nervous System

0.0394

0

3

2

16

0.0314

Non-small cell lung cancer (hsa05223)

Cancers

0.0394

1

5

3

24

0.0028

Pancreatic cancer (hsa05212)

Cancers

0.0413

2

5

3

33

0.0028

Prostate cancer (hsa05215)

Cancers

0.0488

3

3

6

32

0.0003

Focal adhesion (hsa04510)

Cell Communication

0.0525

1

7

9

71

0.0028

Chemokine signaling pathway (hsa04062)

Immune System

0.0582

1

8

7

72

0.0080

Pathways in cancer (hsa05200)

Cancers

0.0582

2

12

15

151

0.0028

Melanogenesis (hsa04916)

Endocrine System

0.0657

2

2

2

26

0.0003

B cell receptor signaling pathway (hsa04662)

Immune System

0.0713

0

5

3

29

0.0314

GnRH signaling pathway (hsa04912)

Endocrine System

0.0732

0

6

6

46

0.0115

Fc epsilon RI signaling pathway (hsa04664)

Immune System

0.0769

0

6

6

33

0.0314

VEGF signaling pathway (hsa04370)

Signal Transduction

0.0769

0

3

0

17

0.0115

ErbB signaling pathway (hsa04012)

Signal Transduction

0.0788

0

5

5

25

0.0314

Acute myeloid leukemia (hsa05221)

Cancers

0.0957

1

3

3

25

0.0028

Gap junction (hsa04540)

Cell Communication

0.0976

0

5

3

42

0.0314

  1. KEGG ID, Kyoto Encyclopedia of Genes and Genomes pathway identifier; P, P-value of association test in the genome-wide study; SNP, single nucleotide polymorphism; SRT P, P-value of permutation test for pathway tested