Table 5

Highest scoring SNP combinations associated with colon cancer using PIA v. 2.0a

Number of SNPs

Scoring Function

Total (Overall)b

%Correct

Sensitivity +Specificity

PPV+NPV

Risk Ratio

Odds Ratio

Gini Index

Probability Difference


1

GSTT1_02

GSTT1_02

PTGS2_11

PTGS2_11

PTGS2_11

IL4_01

GSTT1_02

PTGS2_11

2

CASP8_03

CASP8_03

TGFB1_02

TGFB1_02

TGFB1_02

IL1B_01

CASP8_03

IL1B_01

GSTT1_02

GSTT1_02

PTGS2_11

PTGS2_11

PTGS2_11

IL1B_03

GSTT1_02

IL1B_03

3

MTRR_01

ESR1_03

TGFB1_02

TGFB1_02

TGFB1_02

IL1B_01

IL4_01

IL4_01

IL1B_03

GPX1_03

CDC25A_02

CDC25A_02

CDC25A_02

IL1B_03

MTRR_01

MTRR_01

SOD2_01

GSTT1_02

PTGS2_11

PTGS2_11

PTGS2_11

SOD2_01

DIO1_04

DIO1_04

4

race

race

CHEK1_02

CHEK1_02

CHEK1_02

WRN_03

IL4R_02

ESR1_03

IL1B_01

IL1B_01

TGFB1_02

TGFB1_02

TGFB1_02

IL5_02

SOD2_01

GPX1_06

IL1B_03

IL1B_03

TNF_02

TNF_02

TNF_02

IL10_02

GSTT1_02

CYP19A1_06

MTHFR_02

MTHFR_02

CDC25A_02

CDC25A_02

CDC25A_02

CYP19A1_06

CYP19A1_09

GSTT1_02


a Data were generated using cell counts to assign case versus control status (IFRACT = 0) and excluded the training data when scoring and running 10 10-fold cross-validations for functions 1–5 (ITRAIN = 0, FRACT = 0.1, NTIME = 10).

b Total score is the summation over all scoring functions after linearly scaling the score for each individual function such that the top score is 50.0.

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

Open Data