The plot shows normalized enrichment scores (NES) obtained from GSEA for those cell cycle gene sets with significant enrichment (FWER-adjusted p < 0.05) after GSEA analysis. A positive NES indicates that the gene set is associated with unstressed, tachyzoite parasites, while a negative NES...
Enrichment plots from gene set enrichment analysis (GSEA).ShiuHuey ChouBorSheng KoJiShain ChiouYuehChwen HsuMongHsun TsaiYuChiao ChiuIShing YuShuWha LinHsinAn HouYiYi Kuo
Each gene set was repeatedly permutated 1000 times for each analysis. The nominal p value (NOM-p) and normalized enrichment score (NES) were applied to rank the pathways over-represented in each of phenotypes. GSEA enrichment plots were drawn using ggplot2 package in R. Statistical analysis ...
ISP Terms = immune-system process child terms truth set; RNAseq Terms = top 100 terms from RNAseq analysis of the same cell types. D Bubble plots of the top 10 GO terms as ranked by various gene set testing methods. The size of the bubble indicates the relative number of genes in ...
Gene set enrichment (GSE) analysis is a popular framework for condensing information from gene expression profiles into a pathway or signature summary. The strengths of this approach over single gene analysis include noise and dimension reduction, as wel
Mootha et al. [5] first used the gene-set enrichment analysis (GSEA) method in a study of diabetes, and then Subramanian et al. [6] more fully described GSEA as an analysis method. The GSEA framework is very similar to that of SAFE, except that GSEA uses an enrichment statistic in pl...
To examine the functional complexity of each gene set, we performed a functional enrichment analysis of Gene Ontology (GO) terms using the ToppFunn webserver26. The Hallmark, candidate, non-candidate, and random sets were all analyzed. The number of enriched GO terms (q-value FDR B&Y adjust...
This Python package provides a computationally performant Gene Set Enrichment Analysis (GSEA) implementation of the pre-rank algorithm [1]. GSEApy was used as the reference for the running sum and enrichment score calculation [2]. The algorithm estimates the enrichment score (ES) distribution of ...
GSEAPY: Gene Set Enrichment Analysis in Python. The main documentation for GSEAPY can be found athttps://pythonhosted.org/gseapy An example to use gseapy, please click here:Example Release notes:https://github.com/BioNinja/gseapy/releases ...
Kim SY, Volsky DJ: PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 2005, 6: 144. 10.1186/1471-2105-6-144 Article PubMed Central PubMed Google Scholar Tu K, Yu H, Li YX: Combining gene expression profiles and protein-protein interaction data to infer gene functions. ...