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Table 1 Comparison of the power of the 4 noncollapsing and 2 standard methods

From: Application of noncollapsing methods to the gene-based association test: a comparison study using Genetic Analysis Workshop 18 data

Chromosome

Gene

Power of methods

  

Naïve method

Fisher's method

Simes' method

GSEA method

SKAT

FamSKAT

3

ABTB1

0.015

0.18

0.025

0

0.075

0.01

3

ARHGEF3

0

0

0

0.035

0.005

0.005

3

B4GALT4

0.015

0

0.015

0.035

0.01

0.015

3

BTD

0

0

0

0.015

0

0

3

CXCR6

0

0

0

0.085

0

0

3

DNASE1L3

0.005

0.005

0.005

0.005

0.04

0.01

3

FBLN2

0.005

0

0

0.035

0

0

3

FLNB

0.01

0.015

0

0.03

0

0

3

LOC152217

0.09

0.145

0.135

0

0.275

0.04

3

MAP4

1

1

1

1

1

1

3

NMNAT3

0.005

0.04

0.005

0

0

0

3

PAK2

0.07

0

0.05

0

0

0

3

PDCD6IP

0.005

0

0.005

0.005

0.04

0.03

3

PPP2R3A

0.045

0.01

0.02

0

0.005

0.005

3

PTPLB

0

0

0

0.02

0.005

0

3

SCAP

0.025

0.005

0.04

0

0.045

0.065

3

SEMA3F

0

0

0

0

0

0

3

SENP5

0

0.02

0.01

0.045

0.01

0.005

3

SUMF1

0.085

0.005

0.06

0.01

0.015

0.005

3

TFDP2

0

0

0

0.035

0

0

3

TUSC2

0.005

0

0.055

0

0.02

0

3

ZBTB38

0.01

0.005

0.01

0.02

0.04

0

  1. Power is calculated based on the analysis of the 200 simulated phenotypic replicates. The largest power for each gene is highlighted in bold.