Moreover, sensitivity gene-burden tests considering only those additional carriers identified by WGS (that is, not identified by WES data), 16 of the 23 gene masks with at least five carriers showed a nominally significant association ( P < 0.05) with the target phenotype, indicating that the additional coding variants identified by WGS are likely to be functionally relevant.
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Sentinel variants (defined as the variant in an association signal where no other variants within 1 Mb showed a stronger association) of the novel signals reaching genome-wide significance in the meta-analysis ( P < 5 × 10 −8 ), and nominally significant ( P < 0.05) with consistent direction of effect in each study, were further tested in the replication samples.
As a post hoc analysis, when only patients were considered (and not controls), the same general pattern of results were observed as for the full group, with the relationship between higher polygene scores and lower test accuracy remaining significant at the P =10 −5 threshold, and nominally significant at the P =0.05 threshold.
Therefore, only nominally significant (unadjusted p -value <0.05) rG are reported in the figure.
However, there are over 200 nominally significant between-breed genetic correlations but less than 50 phenotypic correlations compared with an expected error of 20 at p < 0.05.
Eight other structure–function associations were nominally significant (p < .05, uncorrected) across groups: FPN was associated with components reflecting global surface area (ic4; t = 2.2, p = .031), global thickness (ic5; t = 2.2, p = .029), and precentral surface area (ic62; t = 2.7, p = .009), while DMN was associated with cerebellar GMV (ic22; t = −2.3, p = .023), frontal thickness (ic45; t = 2.2, p = .031), temporal GMV (ic50; t = 2.5, p = .013), precuneal GMV (ic58; t = −2.1, p = .041), and fronto-temporal thickness (ic60; t = −2.0, p = .047). 3.3.2.
No methods produced significant genes with |log2 fold-change| > 1 and FDR< 0.05, but the distribution of nominally significant genes at p < 0.05 confirmed that filtering reduces Type I error rates ( Fig. 2 D, Fig.
In a replication study of the 18 novel loci, findings from the HF GWAS in the GBMI multi-ancestry excluding UK Biobank indicate 33.3% (6 of 18) of variants are significant ( p value <0.05/18), 61.1% (11 of 18) are nominally significant ( p value <0.05), and 100% have a beta estimate that is directionally concordant with our meta-analysis (Supplementary Data 20 ).
It is essential to note that all reported P values are merely nominally significant ( P < .05), but none remained statistically significant after Bonferroni correction.
1815 genes were found to be differentially expressed at a nominally significant level (p<0.05); 809 decreased in expression in the KD samples, while 1106 increased.
Considering the modest number of significantly modified genes upon Dek overexpression by adjusted P -value, we performed pathway analysis on genes with nominally significant P -values ( P -value < 0.05).
Predicted impact of ASC-EV-derived miRNAs on cellular processes The enrichment pathway analyses with the miRNA expression correlations and predicted targets was made by matching the top-60 enriched miRNAs in ASC-EVs with predicted mRNA targets in miRWalk (Suppl data 2 , complete list of nominally significant genes, p-value < 0.05 for each miRNA) and subsequent GO enrichment analyses showed a preponderance for mRNAs affected by miR-1290, miR23/27/24 cluster and the miR-15/107 family with no less than 15,870 mRNAs to be targeted by those enriched ASC-EVs-derived miRNAs.
Association analysis was performed on these 7,369 transcripts which resulted in the identification of 461 FDR-significant GA-related transcripts (1,611 nominally significant transcripts; nominal p -value < 0.05).
These 25 marks were tested for association with prostate cancer, and nominally significant associations (p < 0.05) with aggressive prostate cancer were found for all 9 marks near VTRNA2-1 (Table 1 ), with most remaining nominally significant after dichotomising (Supplementary Table 2), (as previously reported, based on the same datasets [ 5 ]).
Further investigation revealed nominally significant enrichment of active enhancers of all three cell types from the connective bone category (including connective cells, fibroblasts, and osteoblasts; all p <0.05; S8 Fig ).
We considered associations as nominally significant at P < 0.05.
ROH hotspots contain genes with diverse functions Regarding the gene content of genomic segments co-localising with both high homozygosity regions and ROH hotspots (CHI4:42,552,375–48,378,207 bp), the functional enrichment analysis highlighted several gene ontology terms with nominally significant enrichment ( P -value < 0.05) (Additional file 7 : Table S5).
There were 202 correlations (out of 1425 possible, 14.2%) that were nominally significant, p < 0.05 before correcting for multiple hypotheses testing.
Logistic regression analysis under the additive genetic model (Table S2 ) revealed 3 nominally significant SNPs with p < 0.05 ( PLG /rs4252120, KIAA1462 /rs2505083, and SLC22A3-LPAL2-LPA /rs2048327) and 2 SNPs showing a trend for association with p < 0.10 ( SORT1 /rs602633 and SMG6 /rs2281727) ( Table 2 ).
For each gene, the genotype score for a randomly chosen common SNP (common variant genotype score, CVGS) was regressed on the unweighted sums of genotype scores for all rare SNPs in the gene (sum of rare variant genotype scores, SRVGS), and the frequency of nominally significant ( P < 0.05) regressions was recorded.
14 We defined replicated SNPs as those showing nominally significant association ( P <0.05) and a consistent direction of effect.
We had 80% power to detect nominally significant associations (p = 0.05) with SNPs that account for at least 0.8% of a trait's variance (full sample) or at least 1.0% of variance (individuals with MRIs).
Notably, the SNPs at 11q12.1 also are nominally significant (P<0.05) in the NFD subgroup, which is different from the observation for the SNPs at 6p21.32.
Regarding descriptive statistics on rumination, gender, age, lifetime psychiatric problems, and present somatic disorders, Supplementary Table 1 shows that except for frequency of pain problems there are differences between the Budapest and Manchester subsamples in all variables at either a nominally significant ( p ≤ 0.05) or trend (0.05 < p ≤ 0.10) level.
Genes associated with kidney function (eGFRcrea, eGFRcys, urea) We compiled a list of 32 genes that were significantly associated with eGFRcrea or eGFRcys either via GBT or ExWAS analyses, and which showed a direction-consistent and at least nominally significant ( p < 0.05) association with the respective other GFR estimate, along with a direction consistent association with urea and CKD (Table 1 ; Supplementary Data 2 ).