collections: Collection of 34,010 annotated gene sets

In cashoes/sear: Simple (effin') enrichment analysis in R

Collection of 34,010 annotated gene sets

Description

A dataset containing >34,000 annotated gene sets from the following sources:

Usage

collections

Format

A data frame with 34,010 rows and 4 variables:

• collection: origin of the gene set (MSigDB: H - hallmark, C1 - positional, C2 - curated, C3 - motif, C4 - computational, C5 - GO gene ontology, C6 - oncogenic, C7 - immunologic; BTM or TISSUES)

• subcollection: collections are sometimes further subdivided (e.g. C2: CP:BIOCARTA, CP:KEGG, CP:REACTOME, etc.)

• geneset: name of the gene set in the collection

• description: a short description of the gene set (only available for some MSigDB collections)

• members_mrna: gene members (using HUGO Gene Nomenclature Committee [HGNC] gene symbols)

• members_mirna: miRNA members (using naming convention used by mirBase; described in: Victor Ambros, Bonnie Bartel, et al. A uniform system for microRNA annotation. RNA 2003 9(3):277-279.)

Details

• MSigDB (33,591): Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America. 2005;102: 15545-15550. doi:10.1073/pnas.0506580102

• Blood Transciptome Modules (BTM; 346): Chaussabel D, Baldwin N. Democratizing systems immunology with modular transcriptional repertoire analyses. Nat Rev Immunol. 2014;14: 271-280. doi:10.1038/nri3642

• Tissue Enrichment (73): Benita Y, Cao Z, Giallourakis C, Li C, Gardet A, Xavier RJ. Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor. Blood. 2010;115: 5376-5384. doi:10.1182/blood-2010-01-263855

Gene set members were also mapped to equivalent validated targetting miRNAs to enable unbiased enrichment analysis of miRNA lists, as described in:

• Godard, P. & van Eyll, J. Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy. Nucl. Acids Res. 43, 3490-3497 (2015).

cashoes/sear documentation built on Feb. 16, 2024, 6:45 a.m.