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It then assesses the category groupings or interval breaks to pick the most significant combination of variables.
The most significant combination was combination 5-6-7 ors9479757-rs2075527-rs1048505757, with global P values of 0.0021 and 0.0514 for SI and ND respectively, Table 4.
We selected a combination of an elevated level of γ-glutamyltranspeptidase (γ-GTP) and an elevated white blood cell (WBC) count as the most significant combination of risk factors for the development of metabolic syndrome.
According to the MDR analysis, the most significant combination was the three-locus model, rs2106809 (ACE2), I/D (ACE), rs1403543 (AGT2R), which had the maximum cross-validation consistency of 10 and was significant at the 0.012 level of P value, as calculated using permutation test.
In principle this method can be generalized to the case of three or more replicates, by choosing m-1 independent pairs among the m replicates, calculating the relative shifts and their respective p-values for these pairs, and combining the p-values using Fisher's method [ 20] to find the most significant combination of shifts.
Three models were used for the association study: (1) conventional GWAS (genome-wide association study), fitting a single SNP effect regardless of subspecies origin, (2) interaction GWAS, fitting an interaction between SNP and subspecies-origin, and (3) best variable GWAS, fitting the most significant combination of SNP and sub-species origin.
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The figure mostly explains the regulation of genes in classes 011 and 111 since these classes are associated with the most significant combinations of cis-regulatory descriptors.
The most significant combinations of loci were, for the two-way combination, TRX1-14 and TRXR2-04 (naïve P=0.00026) and, for the three-way combination, GPX4-02, TRX1-14 and TRXR2-04 (naïve P=0.00021).
We find that the most significant combinations are those which include the triple GOLDCD, FV950 and EMPHETCD, together with one additional variable, the most significant being FIBRINOGEN, BMI, PHLEGM, DWALK and age.
The most significant haplotype combination was with the TLR5 G22A SNP, without the two protective TLR5 SNPs (C100T and T1844C) and with the two TLR4 SNPs (A1571T and G1807A) (p<0.0001).
Table 8 outlines the multilocus genotype frequencies and effect sizes for the most significant SNP combination identified with multifactor dimensionality reduction (GSR-16 and TRXR2-05).
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