Single-Sample Gene Set Enrichment Analysis of Bisphenol-Related Signatures

In our study, we utilized single-sample Gene Set Enrichment Analysis (ssGSEA) as a variant of conventional Gene Set Enrichment Analysis (GSEA). ssGSEA is designed to calculate an enrichment score for each gene set, representing the degree to which the genes in a particular set are coordinately upregulated or downregulated within a sample. This method allows for a more personalized assessment of pathway activity in individual samples, which is particularly useful in studies like ours that investigate the varying impact of environmental factors such as bisphenol A (BPA) across different samples. To conduct the ssGSEA, we first prepared an input file containing normalized gene expression data from our glioma cohort. These data provided the foundational matrix for conducting the enrichment analysis. We then selected a predefined gene list known to be associated with the bisphenol-related signature, which included genes either known or hypothesized to interact with or respond to BPA. ssGSEA then calculated an enrichment score for each sample based on the expression of this bisphenol-related gene set. The enrichment score essentially quantified the degree to which the set of interest was overrepresented at the top or bottom of the ranked list of genes in the sample, reflecting the activation state of the gene set.