“nominally significant”

FUSION first estimates the SNP heritability of steady-state gene and uses the nominally significant ( P < 0.05) genes for training the predictive models.

To obtain stringent TFBS predictions, an empirical score distribution was estimated for each PWM for each species' genome as the set of all nominally significant ( P < 0.05) motif scores identified within the target set of promoter sequences [pwm_scan -s 1 -p ln(0.05)].

We evaluated how well independent pQTLs reported by the INTERVAL study 9 ( n = 3301) replicated in our results and found 75.6% to be both directionally consistent and nominally significant ( P < 0.05) (Supplementary Note 2 and Supplementary Figs. 6 and 7 ).

As suggested by a previous study 4 , most of these lead variants at T2D loci in either the Japanese or European population showed at least nominally significant ( P < 0.05) associations in the alternative population, even if not genome-wide significant, except for variants that were rare or monomorphic in one population such as NKX6-1 rs201597274, HNF1A rs187150787, and PAX4 rs2233580 in the Japanese population and HNF1A rs56348580 in the European population.

All nominally significant associations (P<0.05) are listed.

A scatter plot of SNPs with at least nominally significant ( p < 0.05) effects on both BMI and T2D was generated using RStudio with the ggplot2 package, and Pearson correlation between BMI and T2D-associated signals calculated in R using the cor() function.

Mendelian randomization analysis For sex hormones, the MR IVW estimates for total T [-0.09 (-0.16, -0.01)] in men and bioavailable T [0.13 (0.03, 0.23)] in women were nominally significant ( p <0.05), but they did not pass the significance level of p < 0.0071 after Bonferroni correction.

Of the 46 SNPs, 17 Bonferroni-replicated ( P <0.05/46=0.0011), and 14 additional were nominally significant ( P =0.05); there was a clear distributional enrichment for smaller P -values, e.g., 67% met nominal or better significance, far more than the 2.5% expected by chance (requiring same direction; Supplementary Figure 4 ).

Furthermore, when applying a sequential analysis approach in an N-of-1 framework, we were able to determine that 13 of the 15 individuals with nominally significant systolic blood pressure changes, and 14 of the 18 individuals with diastolic blood pressure changes over six months demonstrated this trend (p < 0.05) by the fifth month of their study enrollment.

Step 5: We generate a ranked list of drug repositioning candidates and MOA categories that show enrichment of nominally significant ( p < 0.05) gene-based associations (MAGMA and S-PrediXcan) across compounds within each category.

A total of 205 risk factor associations were found to be nominally significant ( p < 0.05).

Results Differential expression Overall, 7565 genes were differentially expressed (nominally significant p < 0.05) in small intestinal biopsies between cases with a-CD and controls, and 5244 genes remained differentially expressed after adjusting for multiple comparisons.

The higher relative abundance for these taxa was nominally significant in carriers ( P ≤ 0.05), but non-significant after correction for multiple testing which is not unexpected given the small sample size.

In an earlier study of maternal smoking in Norwegian newborns ( Joubert et al., 2012 ) that identified 26 loci associated with maternal smoking during pregnancy, 19 passed quality control (QC) in our own analysis, and the association between methylation and ethnicity was found to be nominally significant (p<0.05)at 6 (31.6%) CpG loci.

Several genera, including Clostridium, Ruthenibacterium, and Dorea, showed nominally significant associations (p < 0.05).

In SMR analyses of gene expression and migraine within the Finnish cohort, six genes—EP300, HDAC3, SIRT1, AARS2, SLC16A1, and SMARCA4—showed nominally significant associations ( P < 0.05).

Differential gene expression analyses of CD11b + cells in VAT and SAT from individuals with obesity revealed nominally significant differences in the gene expression profile (FDR p < 0.05, absolute fold change > 1.5; Figure 1A,B ).

Using a nominally significant cutoff ( p < 0.05), 30 module-trait relationships emerge, with a range from zero to six significantly correlated modules per trait.

For three cancers (OV, BRCA, LUAD), differential coexpression was nominally significant ( p < 0.05) for all soft thresholds.

Differentially abundant proteins in each group were defined based on the following criteria: Proteins identified in at least 60% of samples in at least one group and nominally significant difference in protein abundance (unadjusted p < 0.05).

A total of 19 HLA alleles had nominally significant maternal and/or fetal effects on BW ( P <0.05; Supplementary Table S7 , available as Supplementary data at IJE online); 13 of the 19 alleles had evidence for a maternal effect only, four alleles primarily had evidence for a fetal effect only and two alleles had evidence of both.

For any medication with a nominally significant association ( p < .05), the same analysis was repeated in the chemotherapy group to test for nonspecific effects.

Notably, though we observed attenuation of the signal after excluding LGD variants, five gene–cancer associations remained nominally significant ( P < 0.05): BRCA1, BRCA2, RAD51B and CHEK2 in breast cancer and BRCA1 in ovarian cancer, (Figure 4 and Supplementary Table S8 ).

The 36 nominally significant miRNAs ( p < 0.05) identified in the PDN/PDD comparison from LIMMA were used to classify disease state (See Figure 2B ), though with more limited accuracy than the PD-control model (absolute error rate = 13.8%, sensitivity = 81.2%, specificity = 88.9%).

We selectively included 44 diseases (excluding cancer, which is a limitation to be noted) in the first part of phenome-wide association analysis (PheWAS) and identified nominally significant associations ( P < 0.05) between the SES-associated variants and CHD.