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Table 5 Mean and standard deviation of the Pearson correlation for the SVR models constructed from subsets of SNPs selected by raw p-values of the simulated database 1.

From: SNPs selection using support vector regression and genetic algorithms in GWAS

Group

SNP selection with raw p-values

# SNPs

Linear**

RBF**

PUK**

1

< 10-9

2a

0.49(0.14)

0.48(0.14)

0.54(0.14)

2

< 10-8

2a

0.49(0.14)

0.48(0.14)

0.54(0.14)

3

< 10-7

2a

0.49(0.14)

0.48(0.14)

0.54(0.14)

4

< 10-6

2a

0.49(0.14)

0.48(0.14)

0.54(0.14)

5

< 10-5

3b

0.49(0.14)

0.55(0.14)

0.56(0.13)

6

< 10-4

3b

0.49(0.14)

0.55(0.14)

0.56(0.13)

7

< 10-3

6c

0.55(0.14)

0.58(0.14)

0.71(0.16)

8

< 10-2

14

0.67(0.13)

0.67(0.13)

0.73(0.12)

9

< 10-1

119

0.49(0.14)

0.55(0.14)

0.56(0.13)

10

< 0.20

220

0.36(0.18)

0.69(0.09)

0.73(0.09)

11

< 0.30

307

0.50(0.09)

0.65(0.07)

0.68(0.06)

12

< 0.40

401

0.60(0.11)

0.69(0.09)

0.72(0.09)

13

< 0.50

511

0.63(0.10)

0.67(0.09)

0.67(0.10)

14

< 0.60

598

0.58(0.10)

0.62(0.10)

0.63(0.11)

15

< 0.70

702

0.54(0.12)

0.58(0.12)

0.57(0.12)

16

< 0.80

803

0.49(0.14)

0.50(0.14)

0.49(0.14)

17

< 0.90

914

0.39(0.16)

0.40(0.17)

0.39(0.17)

18

-

7d

0.64(0.13)

0.97(0.03)

0.96(0.04)

  1. *Raw p-values of the Spearman correlation (without Bonferroni correction).
  2. ** Mean and standard deviation of the Pearson correlation in 10-fold cross validation.
  3. (a) Only SNPs 1 and 10. (b) Only SNPs 1, 10 and 60. (c) Only SNPs 1, 10, 50, 60, 121 and 874. (d) Correct model with 7 relevant SNPs and without redundant SNPs (only SNPs 1, 10, 20, 30, 40, 50 and 60).
  4. For each group defined after the first selection, a model SVR was constructed, evaluated for each kernel, through the Pearson correlation coefficient in 10-fold cross validation. The bold line indicates the best model from the first selection for PUK.