Skip to main content

Table 1 Summary of eQTL mapping results. FDR is estimated using Benjamini–Hochberg procedure

From: A pipeline for RNA-seq based eQTL analysis with automated quality control procedures

Summary

Threshods

ROSMAP

Mayo

MSBB

CommonMind

Effective sample size

NA

334

103

65

200

Gene count

NA

26,663

27,101

29,736

21,511

Variant count

NA

6,736,714

6,932,711

6,937,313

6,703,202

Top PC count

NA

3

3

3

3

Cis-eQTL associations

\(P<1\)

124,877,625

131,696,349

143,560,218

103,667,853

Trans-eQTL associations

\(P<10^{-4}\)

18,617,087

19,594,408

21,324,856

14,353,808

Cis-eQTL associations

\(FDR<0.05\)

3,132,119

516,977

124,675

404,182

Cis-eQTL count

\(FDR<0.05\)

1,515,726

326,652

78,690

306,100

Cis-gene count

\(FDR<0.05\)

21,173

7999

3373

6021

Trans-eQTL associations

\(FDR<0.05\)

163,821

23,200

13,000

9151

Trans-eQTL count

\(FDR<0.05\)

78,894

13,607

6454

8914

Trans-gene count

\(FDR<0.05\)

3079

745

394

203