Simplify method was applied to selected categories to remove highly intersecting terms (threshold = 0.5), and a significance threshold for BH-adjusted enrichment p-values was set to 0.001. Comparison of human d
et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005). Article ADS CAS Google Scholar Noel, M. et al. Probing the CMP-sialic acid donor specificity of two human beta-d-...
Differential expression analysis was performed utilizing the edgeR Bioconductor R package. Statistically significant differentially expressed genes (DEGs) were identified based on a FDR threshold of <0.1 and a logFC threshold of >0.58. Gene set enrichment analysis (GSEA) was performed, using well-...
2.7. Metabolic network analysis The related metabolic pathways in AAN rats were performed by means of the quantitative enrichment analysis algorithm described in metabolite set enrichment analysis (MSEA) method [19]. Visualization of the remarkably disturbed metabolic pathways in AAN rats was performed ...
Univariate analysis can be performed using any of the loaded clinical variables, which can be readily visualized as volcano plots. Multi-group comparisons and adjusting for confounding variables is also supported (refer to examples onwww.lipidr.org). A novel lipid set enrichment analysis is implemen...
As anticipated, the cells from the orga- noid core were enriched for hypoxia hallmark genes as determined by gene set enrichment analysis (GSEA; FDR q value = 3.22 × 10−16) and displayed a signature of the hypoxia-dependent mesenchymal-like 2 (MES2) meta- module defined ...
In order not to compromise peak shapes in chromatographic direction, all reference UPLC/MS/MS spectra are generated in separate runs, which are set up so that ions selected for MS/MS analysis are well separated in elution time. We found the variation in retention times for the method ...
Gene set enrichment analysis of the 155 up-regulated mRNAs showed that the most enriched gene ontology (GO) biological process terms were dealing with cell cycle regulation and the most enriched Kyoto Encyclopedia of Genes and Genomes pathways were p53 signaling and cell cycle. Functional analysis ...
Gene set enrichment analysis (GSEA) indicated that the LXR target genes were highly enriched (Fig. 1a). The elevated expression of canoni-cal LXR target genes, including ABCG5, ABCG8 and ABCA1, was con-firmed by reverse transcription–quantitative PCR (RT–qPCR) (Fig. 1b). Interestingly...
Metabolite set enrichment analysis (MSEA) We performed MSEA tests to determine the metabolic pathways most different between the MGUS and MM groups using the overrepresentation analysis which was based on the enrichment of metabolites in a metabolic pathway compared to the total of annotated metabolites...