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Table 3 Results from PLS regression analysis

From: Pathway analysis for genetic association studies: to do, or not to do? That is the question

SNP-selection strategy

Phenotype

# SNPs

C-V # PLS components*

R2 with 1 PLS component†

Average R2 per SNP‡

SNPs from genes with ASKAT p value ≤ 0.05

DBP-1

9414

1

0.418

7.1 × 10−5

 

DBP-C

10,337

0

0.424

6.2 × 10−5

SNPs from genes in Cytoscape pathway with FDR ≤ 0.05

DBP-1

1239

0

0.333

4.4 × 10−4

 

DBP-C

866

1

0.302

5.2 × 10−4

SNPs from genes in Cytoscape common network

DBP-1

242

0

0.228

1.6 × 10−3

 

DBP-C

239

0

0.197

1.3 × 10−3

  1. *The optimal number of PLS components, as determined by 10-fold cross-validation.
  2. †R2 values for a PLS model with 1 component.
  3. ‡The 1-component R2 divided by the number of SNPs in the PLS component with nonzero regression coefficient, which are 5920, 6835, 759, 580, 143, and 150 SNPs, respectively.
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BMC Proceedings

ISSN: 1753-6561

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