What the reviewer fails to mention is that because 32% of genes do change orientation and given a sample size that will make expectations highly significant, the null hypothesis of no change will be rejected by a more significant P value (P = 10 -113 ) by Fisher test, therefore rejecting the WGD model .
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There were 1,247 in common diseases between the predicted set and text mining hits, representing a highly significant proportion as assessed by hypergeometric test (p = 6.33e-113) (Fig. 4 d; Additional file 7 : Table 3).
P values were highly significant ( P <1 × 10 −112 ).
A hypergeometric test showed that there is an extremely significant overlap (256 CpGs) by our 3084 discovery CpGs with their reported CpGs ( p < 1.29e‐111).
The coefficient of linear correlation between the input and output signals was r = 0.9421, and it was highly significant ( p = 1.46 × 10 –111 ).
Pan‐cancer, the correlation dropped from ρ = 0.52 to a lower, but still highly significant value of ρ = 0.24 ( p = 4.5E‐111) after the control for proliferation.
RNA‐sequencing data further supported these findings, showing a highly significant ( p = 1.22e‐110) increase in HGFR expression in CRC samples relative to normal samples from non‐cancerous patients (Figure 1C ).
Using a subset of 19 metrics, MANOVA analysis revealed the there was a highly significant difference in the structure and dynamics of the plant ER under these treatments (Pillai’s trace, F (72,648) = 17.5, p = 2.7 × 10 −110 ; or Roy’s largest root, F (18,162) = 36.7, p = 7.9 × 10 −48 ).
Meta-analyses of cis -eQTLs for brain-related traits show at least one variant in the ANKDD1B gene to be highly significant in the cortex ( P = 3.18×10 -110 ; Table F in S1 Table ) and nominally significant in the hippocampus ( P =.003; Table G in S1 Table ) [ 26 ].
Therefore, we calculated the statistical probabilities of two-way overlap between exosome and CP190, BEAF-32 or CTCF sites by hypergeometric tests considering only active TSSs of all annotated gene isoforms and indeed observed highly significant overlap over expectation ( P < 3.7 × 10 − 110 for each comparison).
Two loci stood out with highly significant p -values, on chromosome 19 (lead rs58542926, p = 4.4 × 10 −110 ) and chromosome 22 (lead rs738409, p = 2.8 × 10 −161 ), both identified in the GWAS on liver fat.
In addition, although the fold enrichment has a decreasing trend as we consider more vQTLs in the analysis, we still observed substantial and highly significant GxE enrichment even in the top 15% of vQTLs for PA (fold enrichment = 1.66, P = 4.0e-109) and SB (fold enrichment = 1.51, P = 1.5e-87), suggesting pervasive GxE interactions between SNPs associated with BMI variability. vPGS Predicts Population-Level and Within-Individual Variability of BMI.
Since the A and flanking C1 and C2 exons constitute only a small portion of the coding genome (∼10 million nucleotides as per our dataset), this enrichment is highly significant as revealed by a Chi-square test (P<1.99e-108), when comparing the ratios of driver vs. passenger mutations in alternative splicing neighborhoods as compared to the rest of the exome.
As anticipated, lipid ratios capturing PUFA synthesis, namely PE(P-16:0_18:2)/PE(P-16:0_20:4), PE(P-18:0_18:2)/PE(P-18:0_20:4), PE(P-16:0_18:3)/PE(P-16:0_20:5) and PE(P-18:0_18:3)/PE(P-18:0_20:5), exhibited highly significant associations with FADS1/FADS2/FADS3 loci [575 SNPs; top hit: rs174564 for the PE(P-18:0/18:2)/PE(P-18:0/20:4); imputation r 2 = 0.999; beta = 0.49; p-value = 8.07 × 10 −107 ; p-gain = 2.60 × 10 +83 ].
We found that 48% (237/489) of Hoxa2-regulated genes had at least one Hoxa2-bound region assigned to them, which represents a highly significant enrichment compared with all genes ( P = 1.1 e –106) ( Figure 4 A).
Unusually, ChIP-seq identified highly significant, noncanonical binding of DsdC1 FLAG ( P = 1.98 × 10 −106 ) and DsdC2 FLAG ( P = 2.5 × 10 −74 ) both within the coding sequence and directly downstream of the neuO gene, with only a very modest peak being identified within its promoter region ( Fig. 4 A ).
Using these analytic approaches, we found that each of the eight groups of sex-specific genes listed in SM- Table 3 a-3b are jointly and significantly associated with longevity in one sex ( P = 8.7 × 10 −165 ∼1.5 × 10 −37 ), but not jointly significant in the other sex ( P > 0.05), while PRS-sex interaction effects are highly significant ( P = 5.2 × 10 −106 ∼4.4 × 10 −15 ) (SM- Table 5 ).
S2 ): While only 24,303 (5.7%) of the total 427,350 pairs of enzyme-catalyzed reactions are coregulated, 175 (42.9%) of the 408 fully coupled pairs are coregulated, which is highly significant (hypergeometric test, P value = 4.2 × 10 −105 ).
Despite these differences, mRNA and protein levels displayed a highly significant positive Pearson’s correlation coefficient of 0.35 ( p = 3.6 × 10 −104 Figure 1 a).
Next, based on the z score in the latent factor mixed models (LFMMs), we detected 155 CNVs with |z| scores ≥ 10 ( Supplementary Table S11 ) that were highly significant (3.63 × 10 −6 ≥ p values ≥ 1.34 × 10 −103 ), associated with environmental parameters in 47 old sheep populations.
However, notably, even after explicitly controlling for prior treatment time in the Cox regression model, the increased expression in all 48 genes in the mesothelioma prognostic signature is still markedly associated with worse patient survival (Fisher’s exact test for enrichment of overlapping genes between explicitly controlling or not controlling of prior treatment is extremely significant, odds ratio = infinity, p = 1.54e−103).
Among these, MTND2 had highly significant associations across HDL cholesterol, Apolipoprotein A1, LDL and Triglycerides (lowest P = 3.2 × 10 –103 ).
The 212 transcripts reduced in both Caco2 and HUG1N cells depleted of GATA6 represent a highly significant, non-random overlap ( Fig. 4A ; odds ratio 9.0, p <4 × 10 −103 by Fisher exact test) and were enriched for Gene Ontology terms related to the cell cycle, particularly M-phase ( Fig. 4B ).
For example, when considering the 100 top genes most enriched in a cell type, there was a highly significant enrichment in astrocytes (Fold Enrichment (FE) = 1.4e8, p = 4.2e-103), endothelial cells (FE = 1.2e8, p = 2.8e-86), microglia (FE = 1.2e8, p = 2e-86), neurons (FE = 4.2e7, p = 3.7e-30), and oligodendrocytes (FE = 2e8, p = 6.4e-163) across the five data sets.
We also confirmed strong and highly significant associations at the previously described loci, including chromosome 2q24.2 encoding PLA2R1 (rs17831251, OR = 2.25, Meta-analysis P = 4.7 × 10 −103 ) and 6p21.32 encoding HLA-DQA1/DRB1 genes (rs9271573, OR = 2.41, Meta-analysis P = 2.7 × 10 −154 ).