Table 4 Interactive effects between POSTN and SOST genes on BMD variation by MDR and conditional logistic regression analyses   Either LS or FN LS FN SNP of POSTN rs9547970 rs9547970 rs9547970 SNP of SOST rs2301682 rs9899889 find more rs9899889 rs865429 rs865429 rs2301682   MDR Cross validation

learn more consistency 20/20 19/20 20/20 Prediction accuracy 0.57 0.57 0.56 Sign test P-value <0.0001 0.001 0.0087 Conditional logistic regression analysis P value 0.001 0.002 0.002 Several output parameters are used to select the best interaction model in MDR. The cross-validation consistency score measures the degree of consistency with which the reported interaction is identified as the most evident model. The testing accuracy score measures the degree to which the interaction accurately predicts case–control status (accuracy score ≥0.55 is suggested as “interesting”). The best model

is the one with the maximal cross-validation consistency and minimal prediction error. When cross-validation consistency is higher for one model and prediction error is lower for another model, the model involving the fewest loci/factors is taken as the best. The statistical significance (sign test P value) derived empirically from 1,000 permutations was adjusted for multiple comparisons EMSA showed the disappearance of CDX1 binding site in the variant allele of rs9547970 To detect the potential function of the identified variant, we used the FASTSNP program to predict the function of rs9547970 [24]. Bioinformatics analysis Evofosfamide supplier suggests that the allele change (A/G) at rs9547970

should demolish one binding site of CDX1 (caudal type homeobox 1) (MIM 600746). We therefore conducted an EMSA to confirm the potential changes of CDX1 binding to POSTN caused by rs9547970. In the gel shift assay (Fig. 2), the 33-bp oligonucleotides that contained both allelic variants of rs9547970, representing native many and mutated CDX1 binding sites, were assayed with nuclear extract of HEK293 cells transfected with pCMV-CDX1. We found a specific binding of CDX1 from nuclear extract of HEK293 cells transfected with pCMV6-CDX1 to the wild-type site centering the rs9547970 major allele A of POSTN. No binding was observed with oligonucleotide containing the minor allele G. Binding to the major A allele resulted in a complex that was specifically competed by 660-fold excess of unlabeled probe containing the major A allele. The results indicate that the A/G change at rs9547970 demolishes a CDX1 binding site in the POSTN gene. Fig. 2 Electrophoretic mobility shift and competition assays with nuclear extract of HEK293 cells transfected with pCMV-CDX1 and allelic variants of SNP rs9547970 in POSTN.