Statistical values reported by cBioPortal on TCGA PanCancer Atlas data were noted. The number of replicates, statistical tests, and p values are noted for each analysis in the figure legends. Reporting summary Further information on research design is available in the Nature Portfolio Reporting ...
To identify significant cis-eQTL associated with eGenes, we defined the empirical P value of the gene that was closest to an FDR of 0.05 as the genome-wide empirical P value threshold (pt). We obtained the gene-level threshold for each gene from the beta distribution by qbeta (pt, beta...
PathNet relies on two types of evidence in the gene level: direct evidence and indirect evidence [54]. Direct evidence of a gene corresponds to the p value obtained from a statistical test such as a t test when comparing two given phenotypes. Indirect evidence of a gene is calculated from ...
Several eukaryotic proteins associated to the extracellular leaflet of the plasma membrane carry a Glycosylphosphatidylinositol (GPI) anchor, which is linked to the C-terminal residue after a proteolytic cleavage occurring at the so called ω-site. Compu
RNAlysis supports multiple approaches and statistical methods for enrichment analysis, including classic gene set enrichment analysis, permutation tests [20], background-free enrichment analysis [21, 22], and enrichment for ordinal or continuous variables. RNAlysis can automatically retrieve enrichment anal...
All statistical analyses were performed using R software (version 4.0.0; https://www.R-project.org). The difference of immune cell infiltration was assessed by Wilcoxon rank-sum test. For survival analysis, univariate and multivariate Cox analyses were used to explore the prognostic value and ind...
Using this threshold value, we obtain the (l \times k) matrix M, with matrix elements M_{cp} = 1 if country c has an RCA for product p, and zero otherwise. This matrix can be viewed as the incidence matrix of a bipartite network linking countries to products. From this matrix, [63...
Data:Lessons learned from the current pandemic about data, variables and information that should be obtained are critically discussed for specific countries (Grossmann et al.2022; The Royal Statistical Society2021; Rendtel et al.2021) and on a European and international level (Kucharski et al.2021...
Our method not only provided statistical inference of the difference of edge strength between graph nodes in the differential network analysis, but also a multiple testing procedure for simultaneously testing the large number of tests with FDR control to infer the structure of the differential network...
we simulated the growth of 39 soil bacteria on 82 plant exudate metabolites. We developed a theory-based approach to estimate microbial substrate uptake parameters using only genome- and substrate-derived traits. We simulated population-level estimates of key traits, including realized growth rate and...