Table 1. Summary findings of integrative omic analysis of endoxifen sensitivity in HapMap YRI LCLs.
| Phenotype | 3 μM | 5 μM | 7 μM | 10 μM |
| Step1: pheno∼mRNA (p<0.05) | 788 genes | 897 genes | 846 genes | 1117 genes |
| Step2: pheno-miRNA (p<0.05) | 32 miRNAs | 71 miRNAs | 74 miRNAs | 94 miRNAs |
| Step3: mRNA∼miRNA (p≤0.0001) | 13 miRNAs | 33 miRNAs | 45 miRNAs | 56 miRNAs |
| 28 genes | 87 genes | 95 genes | 119 genes | |
| Step 4: mRNA∼SNP (P≤0.0001) | 28 genes | 87 genes | 95 genes | 119 genes |
| 18410 SNPs | 45943 SNPs | 47725 SNPs | 45477 SNPs | |
| Step 5: SNP∼miRNA (p<0.05) | 13 miRNAs | 33 miRNAs | 45 miRNAs | 56 miRNAs |
| 9080 SNPs | 33044 SNPs | 35362 SNPs | 36418 SNPs | |
| Step 6: SNP∼pheno (p≤0.0001) | 4 SNPs | 22 SNPs | 29 SNPs | 23 SNPs |
| 10 miRNAs | 31 miRNAs | 42 miRNAs | 50 miRNAs | |
| 5 genes | 84 genes | 92 genes | 117 genes | |
| Final Associations | 2 SNPs | 16 SNPs | 26 SNPs | 11 SNPs |
| 4 miRNAs | 18 miRNAs | 21 miRNAs | 10 miRNAs | |
| 3 genes | 14 genes | 16 genes | 13 genes |
Six steps of associations among endoxifen sensitivity, SNP genotype, mRNA and miRNA expressions were conducted sequentially for 4 endoxifen treatment concentrations independently. Step 1, the association between the phenotypes of endoxifen sensitivity and ∼13,000 gene/transcript cluster expressions; step 2, the association between the phenotypes of endoxifen sensitivity and 201 miRNA expressions; step 3, the negative correlation between mRNA and miRNA expressions from step 1 and step 2; step 4, the association between mRNA expressions from step 3 and SNP genotypes; step 5, the association between miRNA expression from step 3 and SNP genotypes from step 4; step 6, the association of SNP genotypes from step 5 and the phenotypes of endoxifen sensitivity. The final associations are the SNP genotypes, mRNA and miRNA expressions from the step 6 that correlate with endoxifen sensitivity but also associate each other. Numbers of identified biomarkers were indicated in each step for each phenotype. “3, 5, 7 and 10 μM” represent phenotypes of the 4 concentrations of endoxifen treatment. “Pheno” represents the phenotypes of endoxifen sensitivity.