https://github.com/animesh/gsea
Replicate: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles https://www.pnas.org/doi/10.1073/pnas.0506580102
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Repository
Replicate: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles https://www.pnas.org/doi/10.1073/pnas.0506580102
Basic Info
- Host: GitHub
- Owner: animesh
- License: mit
- Language: Python
- Default Branch: main
- Size: 653 KB
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Metadata Files
README.md
Trying to Replicate GSEA: Subramanian et al. (2005)
This project is trying to replicate the Gene Set Enrichment Analysis (GSEA) methodology as described in the landmark article:
- Subramanian, A., Tamayo, P., Mootha, V.K., et al. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS, 102(43), 15545-15550. https://www.pnas.org/doi/10.1073/pnas.0506580102
Data Sources
All data used in this project are publicly available from the Broad Institute's GSEA/MSigDB resource: - GSEA Example Datasets: https://www.gsea-msigdb.org/gsea/datasets.jsp
Specifically, for the leukemia analysis: - Expression data: Leukemia_hgu95av2.gct - Gene sets: c2.symbols.gmt
Workflow
- Compute a ranked gene list using the signal-to-noise ratio between ALL and AML samples from the leukemia dataset.
- Run a from-scratch GSEA pre-ranked analysis using the ranked list and the C2 (curated) gene sets.
- Compare results to those reported in the original GSEA article.
Current Issue
All tested gene sets return ES=0 and p=1.0. This likely indicates a mismatch between gene symbols in the ranked list and those in the gene sets, or another data integration issue. Resolving this is a current priority for the project.
Files
compute_snr_ranked_list.py: Computes the signal-to-noise ratio ranked gene list from the .gct and .cls files.gsea_preranked_with_fdr_and_plot.py: Runs the GSEA pre-ranked analysis and outputs results and enrichment plots.leukemia_ranked_gene_list.txt: Ranked gene list for GSEA.gsea_preranked_results_with_fdr.csv: GSEA results (ES, p-value, FDR/q-value).gsea_plots/: Enrichment plots for selected gene sets.
References
Owner
- Name: Ani
- Login: animesh
- Kind: user
- Location: Norway
- Company: Norwegian University of Science and Technology
- Website: https://www.fuzzylife.org
- Twitter: animesh1977
- Repositories: 749
- Profile: https://github.com/animesh
A medical graduate from Delhi University with post-graduation in bioinformatics from Jawaharlal Nehru University, India.
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