The power of GSEA relies, in a large part, on the Molecular Signatures Database (MSigDB) that provides tens of thousands of expertly curated and annotated gene sets representing cellular processes, canonical pathways, response signatures, etc., derived from prior studies, public data, and curated...
Title An R Package for Exploring Molecular Signatures Database Version1.0 Description The Molecular Signatures Database('MSigDB')is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis<doi:10.1016/j.cels.2015.12.004>.The'msig'package ...
MolecularSignaturesDatabase(MSigDB)3.0ArthurLiberzon1,AravindSubramanian1,ReidPinchback1,HelgaThor-aldsdóttir1,PabloTamayo1andJillP.Mesirov1,*1BroadInstitute,Cambridge,MA02142,USA AssociateEditor:DrAlexBateman ABSTRACT Motivation:Well-annotatedgenesetsrepresentingtheuniverseofthebiologicalprocessesarecriticalforme...
TheMolecular Signatures Database (MSigDB)in a tidy data frame. This is the updated version of the archived repo of@stephenturner Current version:v2024.1.Hs(Aug 2024). Installation #Install devtools if you don't already have itinstall.packages("devtools")#Just get the datadevtools::install_gith...
Abstract Annotated lists of genes help researchers to prioritize their own lists of candidate genes and to plan follow-up studies. The Molecular Signatures Database (MSigDB) is one of the most widely used knowledge base repositories of annotated sets of genes involved in biochemical pathways, signal...
The Molecular Signatures Database (MSigDB) (Liberzon et al., 2011), originally developed for use with GSEA and now employed by many similar approaches, remains one of the largest and most popular repositories of gene sets. The latest version of MSigDB consists of seven collections C1–C7, whic...
Ranked lists were then analyzed for the enrichment of 50 hallmark gene sets (collection H) obtained from the molecular signature database msigDB, maintained by the Broad Institute, using the ‘plotEnrichment’ and ‘plotfgseaRes’ functions in fgsea and the ‘GSEA’ function in DOSE (nperm =...
We also applied a published breast tumor Cancer-Associated Fibroblast/CAF gene signature32 from the Molecular Signatures Database (MSigDB)33,34 and found it was significantly higher in the Tumor vs DCIS and Prepuberty fibroblasts (Fig. 3b). Fig. 3: Microenvironment subpopulations and gene ...
MSigDB: Molecular Signatures Database MAGEs: Melanoma associated antigens SCGB3A2: Secretoglobin family 3A member 2 ICB: Immune chokepoint inhibitor NKX2-1: NK2 Homeobox 1 TTF-1: Thyroid transcription factor 1 References Haupt S, Caramia F, Klein SL, Rubin JB, Haupt Y. Sex dispar...
Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011;27:1739–40. Article CAS PubMed PubMed Central Google Scholar Bosco MC, Puppo M, Santangelo C, Anfosso L, Pfeffer U, Fardin P, et al. Hypoxia modifies the transcriptome of primary human monocytes: modulation of novel immune-...