“nominally significant”

To explore the utility of this concept in interpreting our KGD data, we mapped the nominally significant KGDs (p ≤ 0.05) identified for each cancer driver gene across all histotypes onto the high-confidence STRING functional interaction network ( Franceschini et al., 2013 ) (see Experimental Procedures ).

After applying the Holm-Bonferroni correction for multiple tests, the comparisons that were nominally significant in the unadjusted analyses lost statistical significance (all adjusted P > .05).

As most results were nominally significant (P < 0.05) but did not meet the stringent corrected threshold (P < 0.005), they are cautiously interpreted as indicating potential trends in the discussion of our findings.

When assessing the relationship between the six individual stress domains and the nine CpG sites, we found that acute life events, financial stress, and lifetime discrimination domains had at least nominally significant associations with all CpG sites ( p < 0.05), while neighbourhood stress, relationship stress, and childhood adversity each had nominal associations with at least six CpG sites (Supplemental Table S5).

We note that although APOE has previously been identified as a AD TWAS gene in microglia 83 , we did not highlight it in our scTWAS results because it did not pass Stage 1 screening, despite nominally significant Stage 2 associations in proliferate, surveilling, and reacting microglia (nominal p -values < 0.05).

Although 75 proteins showed nominally significant abundance differences ( p ≤ 0.05), all corresponding q‐values were 0.99, indicating no statistically robust differences in abundance between PEA and VC at 36 h.

So it should be kept in mind that each individual p value has a one-in-twenty chance of being nominally significant (p < 0.05) purely from random fluctuations.

They first extracted nominally significant signals ( p <0.05) from three GWAS studies (WTCCC, German, and NIMH GAIN datasets; Fangerau et al., 2004 ; Wellcome Trust Case Control Consortium, 2007 ; Baum et al., 2008 ), and prioritized potential candidates based on independent, converging lines of evidence from various bioinformatics resources.

The first 10 PCs were included in FG and FI analyses, and nominally significant PCs ( P <0.05) were added in T2DM analyses.

Differential methylation analysis identified 6095 nominally significant differentially methylated CpG sites (DMCs; p < 0.05, log fold-change > 0.1), associated with 2935 unique genes.

Of those, 38,776 (95%) showed the same direction of effect, 33,128 (81%) also had a nominally significant p value ( p < 0.05), and 25,544 (63%) had an FDR-adjusted p < 0.05 in the BLUEPRINT data (Fig. 1b , Supplementary Data 1 ).

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 ).

There are a total of 74 splicing sites were found to have associations with prostate cancer at the nominally significant level threshold (P < 0.05) with P-HEIDI > 0.01 in the Qi et al. cohort and 14 splicing sites in the GTEx V8 cohort.

Each of the independent variables in the regression models was nominally significant, with p < 0.05.

Additionally, for each of the 594 eGFR signals, we queried further genetic association data relevant to the kidney researcher: (7) To highlight the relevance of a genetic association with creatinine-based eGFR for kidney function rather than creatinine metabolism, we included information on whether the locus association was directionally consistent and nominally significant for blood urea nitrogen (BUN) or cystatin-based eGFR (eGFRcys; i.e. locus lead variant P < 0.05; opposite or same direction of effect for BUN or eGFRcys, respectively; n = 852,678 or 460,826, respectively; yielding 491 of 594 signals validated); (8) Since genetic effects with steeper decline versus more stable eGFR over time might point to particularly deleterious mechanisms for the kidney, we included information on whether the signal showed significant association on eGFR decline (N = 343,339 [ 25 ], yielding 8 decline signals).

However, eight pathways ( Table S2 ), including tryptophan metabolism (increased at intoxication), were nominally significant ( p < 0.05).

Where univariate models of the imaging measures, controlling for age and sex, were nominally significant ( P <0.05), the analyses were repeated using mixed linear models implemented in ASReml-R ( www.vsni.co.uk/software/asreml ), fitting the inverse relationship matrix as a random effect, allowing us to control for familial structure.

A FDR-adjusted P value < 0.05 was considered statistically significant; unadjusted P value < 0.05 was considered nominally significant and unadjusted P value = 0.05 was considered borderline significant.

However, a few nominally significant associations are noticeable: Attention deficit hyperactivity disorder (ADHD) showed the most correlated UDIPs (44 UDIPs) ( p < 0.05) with absolute maximum genetic correlation value of 0.1811 ( p = 0.0003).

We found nominally significant correlations between nausea (SSQ) and Path-Choice (r s = 0.26, p < 0.05), between sensory fidelity (PQ3) and Path-Choice (r s = 0.30, p < 0.05), between interface quality (PQ3) and Fishing (r s = 0.26, p < 0.05), and between somatic concerns (ASI) and Fishing (r s = 0.26, p < 0.05), but none survived correction for multiple testing.

For associations with infections, we visualized the results of all allelic associations which had at least nominally significant p-values (P ≤ 0.05) with at least one infection category or with the “any infection” phenotype.

We test what happens if we select as targets sets of genes that are both within a pathway or a network module that is itself significantly enriched for genetic association to a disease as measured by a GWAS (based on a Pascal gene score threshold) and have a nominally significant (P < 0.05) Pascal gene score to the same disease in the same GWAS.

The conditional analysis shows that 45 (including 42 genes) out of the total 74 (~60.8%) unique associations are still nominally significant when conditioned on known GWAS variants ( p < 0.05, Supplementary Table S4 ).

Markers with nominally significant p-values in one or more cell populations ( P ≤ 0.05; e.g CD39, CD38, Ki-67, PD-1) were visualized in boxplots; statistical significance computed using the linear mixed model were further confirmed using non-parametric Wilcoxon rank sum test.

Six miRNAs were nominally significant ( p < 0.05) in VDAART and three were present in Project Viva.