“nominally significant”

Nominally significant associations (directionality and strength shown by beta estimates) are bolded (p < 0.05) and significant associations after correcting for testing 6 modules and 22 traits (FDR) are bolded and in red.

The associations between CHCHD6 GREX and heart failure were nominally significant in two of the three tissues tested in individuals of European ancestry and one of the three tissues tested in individuals of African ancestry ( P < 0.05).

In addition, there was substantial enrichment of nominally significant associations ( p <0.05) among disease SNPs.

In fact, many known imprinted genes that we failed to identify on the basis of these criteria did show nominally significant ( P < 0.05 without correction for multiple comparisons) DNA methylation differences between diandric and digynic triploids (Table S3 in Additional file 2 ).

Also, the association between sentinel variants in the FoxP1 gene and diagnosis of IPF was nominally significant ( p < 0.05) rather than genome-wide significant.

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).

To verify the reliability of these polygenic associations, we repeated the analyses using PRS comprising only the 108 sentinel genome-wide significant schizophrenia variants 15 , based on the assumption that the effect size estimates of genome-wide significant variants should be less affected by population structure than non-significant variants; 77 of the 104 associated traits were nominally significant ( P < 0.05) based on the PRS comprising only genome-wide significant variants.

All showed a concordant effect direction between the GWAS prospective and GWAS retrospective (p=0·0005, binomial sign test), with six loci nominally significant (GWAS prospective p<0·050) and one significant after Bonferroni correction for the 12 loci (rs3851357, GWAS prospective p=0·0035).

Sex-specific SI Trends during Growth The interaction effect of categorical age (<6 or ≥6 years) and sex on SI was nominally significant ( p = 0.05).

Nominally significant associations ( p < 0.05) were observed for obesity, BMI, dementia, asthma, COPD/asthma-related infections, and serum urate ( Table S20 ).

Gene-based analysis revealed 76 nominally significant ( p ≤ 0.050) longevity-associated genes, and we call these 76 genes the “longevity-associated gene set” (Tables S3 and S4 ).

Broadening our analysis to nominally significant ( P < 0.05) FRASER2 outliers showed that individuals with the dominant disorder have a significantly greater number of nominally significant splicing outliers in blood than controls (mean splicing outliers, 7,072 vs 5,267; two-tailed Mann–Whitney U -test P = 0.0112), whereas individuals with candidate biallelic variants did not (mean, 5,722 vs 5,266; P = 0.695) (Fig. 5a ).

Other effective measures include a count of significant genes [ 6 , 9 ], the ratio of nominally significant (P < 0.05) to non-significant SNPs [ 10 ], max mean and re-standardization of gene measures [ 7 ].

Of these, 10 had significantly different effect sizes ( p -value < 7.8 × 10 −4 , Bonferroni correction for 64 variants) and 22 were nominally significant ( p -value < 0.05).

Three out of 11 HbA 1c -associated SNPs had nominally significant ( p < 0.05) associations with HbA 1c levels in at least one of the three race-ethnic groups, but altogether only four of the 33 possible associations (11 SNPs x three race-ethnic groups) were significant ( p < 0.05).

Specifically, we identified a total of 169 nominally significant enriched terms ( p -value < 0.05 and FDR < 0.2), which represent a medium-confidence set, including a subset of 37 high-confidence terms that passed multiple test correction with an FDR of <0.05 ( Figure 3 ).

Implementation of risk variables in models for different clinical contexts To determine which variables predict disease risk, we assigned a score to each variable by (1) using 10-fold cross-validated lasso regression to select the optimal model as a function of the tentatively replicated variables [ 15 ], (2) assigning one point to the variables that were retained and nominally significant ( p < 0.05) and (3) bootstrapping the previous steps 100 times.

Using the GSE21032 hypoxia-associated genes there were 5,348 drugs with negative z-scores, of which 2,405 were nominally significant ( p < 0.05).

Of the 118 disease signatures tested, 12 showed a nominally significant association ( p < 0.05) with at least one of the three dichotomized PCS scores (Table 2 ).

Three further SNP‘s showed nominally significant interactions ( p < 0.05).

Fourteen MGSs were nominally significant for the broad spectrum (Wilcoxon signed-rank test, unadjusted p < 0.05).

Differences between groups were nominally significant (nominal P < 0.05) if the 95% confidence interval [CI] of the group difference did not include the null value (0 for mean differences and 1 for odds ratios), but for the sake of convenience, if the nominal P ‐value in the secondary analysis is less than 0.05, it is described as significant, and if it is 0.05 or more, it is described as non‐significant.

Differentially methylation CpG sites The epigenome-wide differential methylation analysis revealed 26982 CpG sites that differed between obese and lean individuals with nominally significant p-values (p ≤ 0.05).

SNPs on SLC17A3 , SLC22A10 , SLC22A8 , SLC22A11 and ABCC4 were nominally significant at P ≤ 0.05 (Table 1 ).

For all nominally significant associations (P < 0.05), we conducted a Bayesian colocalisation analysis to determine whether GWAS and expression quantitative trait locus (eQTL) signals shared a causal variant [ 40 ].