Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
By Jüri Reimand, Ruth Isserlin, V. Voisin, Mike Kucera, Christian Tannus-Lopes, Asha Rostamianfar, Lina Wadi, Mona Meyer, Jeff Wong, Changjiang Xu and 2 more. Nature Protocols, 2019
1,618 citations recorded by the source corpus.
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists generated from genome-scale (omics) experiments. This method identifies biological pathways that are enriched in a gene list more than would be expected by chance. We explain the procedures of pathway enrichment analysis and present a practical step-by-step guide to help interpret gene lists resulting from RNA-seq and genome-sequencing experiments. The protocol comprises three major steps: definition of a gene list from omics data, determination of statistically enriched pathways, and visualization and interpretation of the results. We describe how to use this protocol with published examples of differentially expressed genes and mutated cancer genes; however, the principles can be applied to diverse types of omics data. The protocol describes innovative visualization techniques, provides comprehensive background and troubleshooting guidelines, and uses freely available and frequently updated software, including g:Profiler, Gene Set Enrichment Analysis (GSEA), Cytoscape and EnrichmentMap. The complete protocol can be performed in ~4.5 h and is designed for use by biologists with no prior bioinformatics training. This protocol describes pathway enrichment analysis of gene lists from RNA-seq and other genomics experiments using g:Profiler, GSEA, Cytoscape and EnrichmentMap software.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/a9e79fb4f8273c847f91655f786ff12cb1a1ba0c
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Citations in the corpus
- Cytoscape Automation: empowering workflow-based network analysis (2019, methodology): “…GitHub has become a common tool in many biologists ’ toolbelt, and A working example is a 2019 Bader Lab pathway enrichment analysis paper [42] where R-based Cytoscape Automation is delivered as supplementary material (protocol 3), and the full workflow is delivered in the GitHub…”
- neuromaps: structural and functional interpretation of brain maps (2022, methodology): “In adjacent fields, such as bioinformatics, there already exist multiple widely-used computational methods for functional profiling and pathway enrichment analysis of gene lists [6, 61].”
- g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) (2019, background): “…as well as in Canada and USA and plays a central role in a recently published pathway enrichment analysis and visualization of omics data protocol (38). g:Profiler is also a major component of an enrichment analysis based automatic clustering tool funcExplorer that benefits on pro-grammatic…”