MSigDB Gene Ontology sets

Gene sets from the Molecular Signatures Database (MSigDB). Used for Fast Gene Set Enrichment Analysis (FGSEA).

MSIGDB_PATHWAYS

Format

A data.frame with 5106 rows and 5 columns:

gs_subcat

character; the database to which the gene set belongs. One of "GO:BP", "GO:MF", or "GO:CC".

gs_exact_source

character; unique gene set identifier.

gs_description

character; gene set description.

entrez_gene

numeric list; Entrez gene identifiers in each set.

set_size

numeric; gene set size. Lengths of entrez_gene.

Details

Gene Ontology (Biological Process, Cellular Component, Molecular Function) pathways from version 7.5.1 of the Molecular Signatures Database (MSigDB). Obtained via msigdbr (organism = "Rattus norvegicus") and reformatted. Prefiltered to pathways with at least 15 and no more than 300 genes. Filtering by size was done because smaller gene sets tend to be less reliable, while larger gene sets tend to be less interpretable.

References

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics, 25(1), 25–29. https://doi.org/10.1038/75556

Dolgalev, I. msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format. R package version 7.5.1, https:://igordot.github.io/msigdbr

Gene Ontology Consortium (2021). The Gene Ontology resource: enriching a GOld mine. Nucleic acids research, 49(D1), D325–D334. https://doi.org/10.1093/nar/gkaa1113

Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015). The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell systems, 1(6), 417–425. https://doi.org/10.1016/j.cels.2015.12.004