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Table 5 Loci-sets with unadjusted p-value no greater than 0.1% in the antihypertensive response example

From: GLOSSI: a method to assess the association of genetic loci-sets with complex diseases

Loci-set

MsigDB ID

No. SNP

No. relevant gene

p-value

q-value

Non-Hispanic white

     

   TPO signaling pathway

c2:338

48

10

0.0001

0.035

   Erk1/Erk2 Mapk signaling pathway

c2:178

74

16

0.0001

0.035

   Sprouty regulation of tyrosine kinase signals

c2:316

36

10

0.0001

0.035

   Multiple antiapoptotic pathways from IGF-1R signaling lead to bad phosphorylation

c2:214

24

8

0.0002

0.035

   PTEN pathway

c2:557

30

8

0.0002

0.035

   Transcription factor CREB and its extracellular signals

c2:152

83

16

0.0002

0.035

   Growth hormone signaling pathway

c2:198

50

11

0.0002

0.035

   PTEN dependent cell cycle arrest and apoptosis

c2:292

24

8

0.0003

0.035

   Upregulated in acute rejection transplanted kidney biopsies

c2:834

132

25

0.0003

0.035

   IL 3 signaling pathway

c2:223

18

6

0.0003

0.035

   Trka receptor signaling pathway

c2:339

41

5

0.0003

0.035

   IL-2 receptor beta chain in T cell activation

c2:222

40

11

0.0004

0.035

   B cell antigen receptor

c2:569

49

18

0.0004

0.035

   IL 4 receptor signaling in B lymphocytes

c2:563

39

12

0.0004

0.035

   Calcium signaling by HBx of Hepatitis B virus

c2:569

16

4

0.0005

0.035

   Glycogen processing

c2:602

39

8

0.0005

0.035

   IGF-1 signaling pathway

c2:213

31

9

0.0005

0.035

   Down regulated following Apc loss

c2:1048

156

32

0.0005

0.035

   Liver selective

c2:979

300

104

0.0005

0.035

   TrkA receptor

c2:559

19

6

0.0006

0.035

   Inhibition of cellular proliferation by gleevec

c2:199

37

10

0.0006

0.035

   IL 6 signaling pathway

c2:226

25

8

0.0006

0.035

   Insulin signaling pathway

c2:229

26

8

0.0007

0.039

   Upregulated in fibroblasts following infection with human cytomegalovirus

c2:1269

131

24

0.0008

0.040

   Down regulated by both curcumin and sulindac in SW260 colon carcinoma cells

c2:1412

50

10

0.0010

0.047

   Upregulated by TPA in resistant HL-525 cells

c2:1679

90

19

0.0010

0.048

African American

     

   Upregulated by UV-B light in epidermal keratinocytes

c2:1717

55

12

0.0004

0.56

   Upregulated in well functioning transplanted kidney biopsies

c2:836

1347

285

0.0009

0.63