BootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses.

ABSTRACT: Introduction: Gene set enrichment analysis (GSEA) subsequent to differential expression analysis is a standard step in transcriptomics and proteomics data analysis. Although many tools for this step are available, the results are often difficult to reproduce because set annotations can change in the databases, that is, new features can be added or existing features can be removed. Finally, such changes in set compositions can have an impact on biological interpretation. Methods: We present bootGSEA, a novel computational pipeline, to study the robustness of GSEA. By repeating GSEA based on bootstrap samples, the variability and robustness of results can be studied. In our pipeline, not all genes or proteins are involved in the different bootstrap replicates of the analyses. F

SUBMITTER: Hemandhar Kumar S 

PROVIDER: S-EPMC11021641 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature