These results show that all four topological measures provide highly significant ( p -value < 1e-16) enrichment in pathogen targets, with betweenness and clustering coefficient displaying highest enrichment, thereby demonstrating the added value of incorporating PPI data into inferred networks for a generalizable approach to identify target regulatory nodes within networks.
Excerpts
We have applied a statistical test and found that all of the comparisons of short gene expression to longer gene expression are highly significant (p-values <10-16, Kolmogorov-Smirnov test).
However, the overlap between the two categories of the intergenic transcribed regions is highly significant (P-value < 10 -16 , chi-square test)." Contributor Information Philipp Kapranov, Email: philippk08@gmail.com.
The network showed strong biological relevance with highly significant enrichment ( p -value < 1.0e-16).
The difference between the two distributions was highly significant ( p < 10 −16 , two-sided Wilcoxon rank-sum test).
The difference in the maximum likelihood (ML) values for the GTR + Γ and JC models was very large (Δln L = 14757.9) and highly significant ( P < 10 −16 ).
By a STRING protein-protein interaction network analysis of proteins identified by MS, we determined a highly significant network of proteins being bound to the nimtRNA transcript ( p < 1.0e−16).
Notably, only proteins associated with our list of cKO- Eed -MADM–specific DEGs, but not sparse Eed -MADM–specific DEGs, formed a highly significant and densely connected network (PPI enrichment P value < 1 × 10 −16 ) (fig.
Changes in mean activation magnitude in both regions between unscaled and scaled t-values are of the order of 10% of unscaled activation magnitude and are highly significant (a t-test over all voxels yields a p-value of p < 10 − 16 ).
This yielded a PPI with 235 edges with an extremely significant enrichment p -value < 1.0e−16 ( Fig. 10 ).
Statistical analysis (MANOVA) of the original data obtained from the cell populations indicated a highly significant difference between them (p<10 −16 ) suggesting that the nuclear SIRT1 pattern reflects structural differences in the nuclei between the cell populations.
The association of ZEB1 with promoters as well as with CpG islands and exonic regions is highly significant at a genome-wide scale (p < 10 −16 , Supplementary file 1D [ Gubelmann et al., 2014 ]).
There is a highly significant correlation between F ST and A ancestry difference between the lowland and highland samples (Spearman's ρ = 0.26, P < 10 −16 ).
This detrimental effect of antibiotics was highly significant among the phyla Bacteroidota and Firmicutes_A (p < 1e–16, OR 0.7) and observed at various host ages ( Figure S2 E).
The correlation is weakly negative ( R S = −0.18) but highly significant ( p <10 −16 ) because the number of points is so large.
Twenty-four GST peptide isoforms were identified under seven different classes with a highly significant protein-protein interaction between GST groups and within other detoxification metabolism-related peptides ( p -value < 1.0 × 10 −16 ).
However, the overlap between the two categories of the interagency transcribed regions is highly significant ( P -value < 10 -16 , chi-square test).
We do detect a highly significant enrichment of marine-freshwater differentially expressed genes, as predicted ( P < 10 −16 ).
The correlation between HNRNPK binding events and nuclear enrichment was highly significant when controlling for transcript length and expression levels (R=0.2, P<10 -16 in HepG2 cells and R=0.07, P<10 -16 in K562 cells).
The network displayed an average target degree of 4.97 and a local clustering coefficient of 0.514, indicating a highly significant PPI enrichment (p-value <1.0e-16).
Furthermore, we validated rhythmicity using two alternative detection methods [RAIN (Thaben & Westermark, 2014 ) and ARSER (Yang & Su, 2010 )], which showed a highly significant overlap between the groups ( Appendix Fig S1G ; two‐sided Fisher's exact test, P < 10 −16 for every pairwise comparison).
In other words, organisms sampled from a defined skin habitat were more similar to each other in 16S sequence than expected for a global background; this enrichment was statistically highly significant (p<<10 −16 , one-sided Mann-Whitney-U test, see Table S1 ).
For a random protein set of comparable size, the expected number of edges was 8, whereas the observed network contained 44 interactions, resulting in a highly significant PPI enrichment p -value < 1.0 × 10 −16 .
We also created protein interaction networks of non-plaque tissue DS, EOAD, and LOAD proteomes, which showed a highly significant degree of protein–protein interactions (PPI enrichment p = 1 × 10 −16 , Supp.
The resulting network showed a highly significant interaction among the proteins (p value < 1.0e −16 ).