Sampling fraction is defined as the ratio of expected abundance in a sample to the corresponding absolute abundance in the ecosystem, which could be empirically estimated by the ratio of library size to the microbial load.aDifferences in sampling fractions introduce false negatives. In this toy exam...
with another 19 (50%) assigned to the luminal B subtype. The remaining four (8%) ER+HER2−samples were assigned to the basal-like subtype. Three clinical HER2+samples were included in this dataset
E–F Scatter plot of liver metabolites between the Yinsyn+BGZ and Yinsyn groups determined by OPLS-DA in ESI- mode (E) and ESI + mode (F). G Heatmap of the metabolites identified. Color depth represents the variation trend of the relative abundance of metabolites, the red color ...
However, an N-terminal proteolytic fragment of VCAN, versikine, arising through the actions of ADAMTS-4 and other versicanases, conversely regulates cross-presenting type 1 conventional dendritic cell (cDC1) abundance and activation in the TME, to promote immune cell trafficking to the tumor and ...
BADGE: a novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data. BMC Bioinformatics. 2014;15(S9):S6. PubMed PubMed Central Google Scholar Wang C, Sun D, Huang X, Wan C, Li Z, Han Y, et al. Integrative analyses of single-cell transcriptome ...
The abundance of proteins co-purifying with the selected target bait proteins was compared between control and oxidative stress-induced (sodium arsenite treatment) cells followed by functional analysis using different bioinformatic tools. B Immunoprecipitation of native, endogenous bait proteins using anti-...
abundance of allele-specific reads was estimated by summing up the number of 129- and Cast-specific reads of all exonic single-nucleotide polymorphism (SNPs) within the gene33. For each gene in our data set, we used the total counts of 129/Sv (N129) and Cast/Ei (NCast) allele-specific...
4D), activity was normalized to bait protein abundance (Fig. 4E, supplemental Fig. S7, supplemental Table S5). The normalized enzymatic activity of SIN3B_1-purified samples was consistently lower than purified complexes containing recombinant SIN3B_2 (Fig. 4E). These data provide additional ...
(not applicable to TMT data, as indicated by “NA” in Fig.4b), except for spt_DIA (LFQ works a little better than dlfq), followed by LFQ. Under the setting, FG_TMT, the TMT-Integrator abundance (abd) is better than the Philosopher intensity (phi) or TMT-Integrator ratio (ratio)...
Nine cytokines showed statistically significant differences in abundance between the disease-association groupings of metabolites (Kruskal–Wallis test corrected by Benjamini–Hochberg FDR q value < 0.10), including IL-6, MIP-1β, IL-12p70, IL-9, RANTES, IL-12p40, MCP-1, IL-1β, and ...