Table 6

Top 10 most frequently observed SNP-pairs in the 100 highest scoring triplet SNP combinations associated with colon cancera.

SNP Pair

Frequency of SNP Pair Observed in Each Scoring Function and Overall

SNP-1

SNP-2

%Correct

Sensitivity +Specificity

PPV+NPV

Risk Ratio

Odds Ratio

Gini Index

Probability Difference

Total (Overall)


IL1B_01

IL1B_03

9

7

0

0

1

71

3

91

CASP8_03

GSTT1_02

20

21

4

0

4

0

3

52

CHEK1_02

TGFB1_02

0

0

14

17

14

0

0

45

MTRR_01

SOD2_01

9

9

3

0

3

4

11

39

CDC25A_02

PTGS2_11

0

0

10

12

10

0

0

32

CHEK1_02

CDC25A_02

0

0

10

11

10

0

0

31

CHEK1_02

PTGS2_11

0

0

8

8

8

0

0

24

CHEK1_02

ALOX5_07

0

0

7

7

7

0

0

21

IL4_01

XRCC1_1

4

7

3

0

3

1

2

20

MTRR_01

DIO1_04

3

3

1

0

1

3

9

20


a Top 100 triplet SNP combinations were generated using cell counts to assign case versus control status (IFRACT = 0). The training data were excluded in scoring and running ten 10-fold cross-validations for functions 1–5 (ITRAIN = 0, FRACT = 0.1, NTIME = 10). If the SNPs were randomly assigned to the top 100 triplet models, a given pair is expected to be observed 3.3 times overall.

Mechanic et al. BMC Bioinformatics 2008 9:146   doi:10.1186/1471-2105-9-146

Open Data